diff --git a/.gitignore b/.gitignore index c667a41e000..c2974194435 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,15 @@ .pydevproject .project LICENSE_HEADER +*.eb.bak_* *.pyc *.pyo *.nja +*.out build/ dist/ *egg-info/ +.venv/ *.swp *.ropeproject/ eb-*.log diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e687bf442f8..af2e74ae887 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,178 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 19,985 easyconfig files, for 3,552 different software packages, -incl. 40 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 20,670 easyconfig files, for 3,670 different software packages, +incl. 41 different (compiler) toolchains. + + +v4.9.4 (22 September 2024) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 14 new software packages: + - Biotite (#21026), chopper (#21418), CLUMPP (#21329), cramino (#21382), dub (#21378), ESM3 (#21026), GOMC (#21008), + MOKIT (#21352), nanoQC (#21371), phasius (#21389), PyBullet (#21356), rnamotif (#21336), versioningit (#21424), + xskillscore (#21351) +- added additional easyconfigs for various supported software packages, including: + - awscli 2.17.54, BiG-SCAPE-1.1.9, ccache 4.10.2, CLHEP 2.4.7.1, CREST 3.0.2, decona 1.4-2024073, dftd4 3.7.0, + GATE 9.4, Gdk-Pixbuf 2.42.11, Geant4 11.2.2, Geant4-data 11.2, Ghostscript 10.03.1, GitPython 3.1.43, + GObject-Introspection 1.80.1, HarfBuzz 9.0.0, ImageMagick 7.1.1-38, JasPer 4.2.4, joypy 0.2.6, Julia 1.10.4, + LDC 1.39.0, Leptonica 1.84.1, Markdown 3.7, MPICH 4.2.2, NanoComp 1.24.0, nanoget 1.19.3, nanomath 1.4.0, + NanoPlot 1.43.0, Pango 1.54.0, PCAngsd 1.2, Pillow 10.4.0, python-isal 1.7.0, pocl 6.0, PROJ 9.4.1, protobuf 28.0, + protobuf-python 5.28.0, R-tesseract 5.2.1, RepeatMasker 4.1.7-p1, RHEIA 1.1.11, RMBlast 2.14.1, + scikit-build-core 0.10.6, sleuth 0.30.1, SNAP-ESA 10.0.0, tesseract 5.3.4, Triton 2.1.0, TurboVNC 3.1.2, + VirtualGL 3.1.1, zlib-ng 2.2.1 +- minor enhancements, including: + - enable support for Apache ORC to Arrow v14.0.1 and v16.1.0 (#21056) + - use proper dependency for tensorboard in easyconfigs for TensorFlow v2.15.1 (#21337) +- various bug fixes, including: + - account for crates for easyconfigs using Cargo-based easyblock when determining checksums for patches in easyconfigs test suite (#21419) + - avoid missing symbol in mclust extension of R-4.0.3 w/ foss/2020b (#21429) + - fix build of librosa 0.10.1 in some environments by removing "python -m build" for soxr extension (#21434) + - fix repeated sanity check runs in manta easyconfigs (#21435) + - fix test_easyconfig_locations when easyconfigs index is present (#21394) + - use proper dependency for libnsl in git-annex (#21441) + - avoid writing into ~/.stack directory during build for git-annex (#21452) +- other changes: + - remove exts_default_options from TensorFlow 2.3.1 (#21290) + + +v4.9.3 (14 September 2024) +-------------------------- + +update/bugfix release + +- added easyconfigs for foss/2024a (#21100) and intel/2024a (#21101) common toolchains +- new toolchain: gmpflf/2024.06 (#20882) +- added example easyconfig files for 107 new software packages: + - absl-py (#21039), accelerate (#21107), affogato (#20636), APOST3D (#21133), bayesian-optimization (#21301), + BayesOpt (#21261), BGEN-enkre (#15752), bitsandbytes (#21248), bliss (#21206), cfgrib (#21113), CLANS (#21099), + colorize (#20964), CORSIKA (#20693), COSTA (#20989), coxeter (#21254), Critic2 (#20833), crypt4gh (#20870), + dblatex (#21207), dictys (#21166), DL_POLY_Classic_GUI (#20819), EGA-QuickView (#20870, #20888), EMMAX (#21174), + empanada-dl (#20454), empanada-napari (#20454), ESIpy (#21006), fastfilters (#21003), fish (#21345, #21381), + flash-attention (#21083), Flax (#21039), fonttools (#21363), fsm-lite (#20503), GDMA (#21171), GeoDict (#20650), + GPflow (#21172), gtk-doc (#21207), Gubbins (#20413), Gymnasium (#20420), HERRO (#21252), IEntropy (#20808), + ilastik-napari (#21003), IMAGE (#20994), junos-eznc (#21166), jupyter-collaboration (#20741), + jupyter-vscode-proxy (#20876), langchain-mistralai (#20759), langchain-openai (#20711), LRBinner (#21310), + lrcalc (#21339), MAGIC (#20900), mallard-ducktype (#21127), MATES (#21229), MBX (#21155), mcqd (#21283), + MeshLab (#20806), meteogrid (#20921), micro-sam (#20636), miniprot (#21157), napari-denoiseg (#20934), + NECAT (#21359), nellie (#21267), NextPolish (#21265), nifty (#20636), ome-types (#21256), openai-python (#20711), + OpenForceField-Toolkit (#20852), orjson (#20880), PEcAn (#21227), PretextMap (#20790), PyBEL (#20953), + pyMBE (#21034), pystencils (#20889), python-blosc (#20636), python-elf (#20636), rankwidth (#20788), Rasqal (#21207), + Redland (#21227), Regenie (#15752), rMATS-long (#20916), Sagemath (#21365), scCustomize (#20907), SCENICplus (#21085), + scFEA (#20777), sdsl-lite (#20503), SharedMeatAxe (#21303), Single-cell-python-bundle (#20116), SIRIUS (#20989), + sirocco (#21304), SKA2 (#20411), SpFFT (#20989), spla (#11607), Stable-Baselines3 (#20884), submitit (#21103), + SVDSS2 (#20855), tdlib (#21305), torch-em (#20636), Umpire (#20989), Uni-Core (#21182), vigra (#20636), + Visit (#20981), weblogo (#20800), wradlib (#21110), xtb-IFF (#20783), yell (#20964), yelp-tools (#21127), + yelp-xsl (#21127), z5py (#20636), Zoltan (#21324) +- added additional easyconfigs for various supported software packages, including: + - AGAT 1.4.0, ASE 3.23.0, Abseil 20240722.0, Albumentations 1.4.0, AlphaPulldown 2.0.0b4, AlphaPulldown 2.0.0b4, + AmberTools 26.3, Arrow 16.1.0, alsa-lib 1.2.11, archspec 0.2.4, attr 2.5.2, BayesTraits 4.1.2, BeautifulSoup 4.12.3, + Biopython 1.84, Boost.MPI 1.83.0, bcl-convert 4.2.7-2, beagle-lib 4.0.1, biom-format 2.1.16, byacc 2.0.20240109, + CDO 2.3.0, CFITSIO 4.4.1, CUDA-Samples 12.2, CUDA 12.5.0 + 12.6.0, CUTLASS 3.4.0, Catch2 2.13.10, CellOracle 0.18.0, + Clang 18.1.8, Coreutils 9.5, chewBBACA 3.3.9, code-server 4.90.2, connected-components-3d 3.14.1, cooler 0.10.2, + cryptography 42.0.8, cutadapt 4.9, cyvcf2 0.31.1, dorado 0.7.3, dtcmp 1.1.5, ESMF 8.6.1, EvidentialGene 2023.07.15, + Extrae 4.2.0, ecBuild 3.8.5, elfutils 0.191, FFmpeg 7.0.2, FLAC 1.4.3, FUSE 3.16.2, Flask 3.0.3, Flye 2.9.4, + FriBidi 1.0.15, ffnvcodec 12.2.72.0, flatbuffers-python 24.3.25, flatbuffers 24.3.25, fmt 10.2.1, fpylll 0.6.1, + GCC 14.2.0, GDAL 3.9.0, GEOS 3.12.1, GHC 9.10.1, GLM 1.0.1, GLib 2.80.4, GLibmm 2.72.1 + 2.75.0 + 2.77.0 + 2.78.1, + GPAW 24.6.0, GetOrganelle 1.7.7.1, Guile 2.0.14 + 3.0.10, Gurobi 11.0.2, gap 4.13.0, genomepy 0.16.1, gensim 4.3.2, + gffutils 0.13, gh 2.52.0, git-annex 10.20240731, gmpy2 2.2.0, googletest 1.15.2, graph-tool 2.59, HDBSCAN 0.8.38.post1, + HOMER 4.11.1, HTSeq 2.0.7, HiCMatrix 17.2, Highway 1.2.0, Hypre 2.31.0, hatchling 1.24.2, histolab 0.7.0, + hypothesis 6.103.1, IQ-TREE 2.3.5, ImageMagick 7.1.1-34, Imath 3.1.11, IsoQuant 3.5.0, igraph 0.10.12, imageio 2.34.1, + imbalanced-learn 0.12.3, inferCNV 1.21.0, intervaltree 0.1, JsonCpp 1.9.5, Julia 1.10.4, jax 0.4.25, json-fortran 8.5.2, + Kent_tools 468, LLVM 18.1.8, LittleCMS 2.16, libdrm 2.4.122, libdwarf 0.10.1, libedit 20240517, libgeotiff 1.7.3, + libgit2 1.8.1, libopus 1.5.2, libsigc++ 3.6.0, libspatialindex 2.0.0, libunistring 1.2, libunwind 1.8.1, libwebp 1.4.0, + libxslt 1.1.42, libzip 1.10.1, lwgrp 1.0.6, lxml 5.3.0, MCR R2024a, MPICH 4.2.1, MUMPS 5.7.2, MariaDB 11.6.0, + Maven 3.9.7, Mercurial 6.8.1, Mesa 24.1.3, Miniconda3 23.10.0-1, MultiQC 1.22.3, makedepend 1.0.9, matplotlib 3.9.2, + maturin 1.6.0, medaka 1.12.1, meshio 5.3.5, meson-python 0.16.0, mm-common 1.0.6, NanoCaller 3.6.0, Normaliz 3.10.3, + n2v 0.3.3, nano 8.1, ncbi-vdb 3.1.1, nettle 3.10, nsync 1.29.2, numexpr 2.9.0, ORCA 6.0.0, OpenEXR 3.2.4, OpenFOAM 12, + OpenFOAM v2406, OpenJPEG 2.5.2, Optax 0.2.2, Optuna 3.6.1, PaStiX 6.3.2, Perl-bundle-CPAN 5.38.2, Pillow-SIMD 10.4.0, + Pint 0.24, Platypus-Opt 1.2.0, PostgreSQL 16.4, PyAEDT 0.9.9, PyCharm 2024.1.6, PyRosetta 4.release-384, + PyWavelets 1.7.0, PyYAML 6.0.2, Pygments 2.18.0, Pylint 3.2.5, Pyomo 6.7.3, Python-bundle-PyPI 2024.06, packmol 20.14.4, + pagmo 2.19.0, parallel 20240722, pixman 0.43.4, pod5-file-format 0.3.10, poetry 1.8.3, popt 1.19, pretty-yaml 24.7.0, + primecount 7.14, psycopg 3.2.1, pyGenomeTracks 3.9, pybind11 2.12.0, pycocotools 2.0.7, pydantic 2.7.4, pygmo 2.19.5, + pyperf 2.7.0, pyseer 1.3.12, pysteps 1.10.0, QuantumESPRESSO 7.3.1, Qwt 6.3.0, R-bundle-CRAN 2024.06, R 4.4.1, + RDKit 2024.03.3, RapidJSON 1.1.0-20240409, Ray-project 2.9.1, ReFrame 4.6.2, Rust 1.79.0, redis-py 5.0.9, + regionmask 0.12.1, rjags 4-15, rpmrebuild 2.18, SDL2 2.30.6, SHAP 0.43.0, SIP 6.8.3, SRA-Toolkit 3.1.1, + STAR 2.7.11b_alpha_2024-02-09, STRUMPACK 7.1.0, SVDSS2 2.0.0-alpha.3, Safetensors 0.4.3, Salmon 1.10.3, + SciPy-bundle 2024.05, SeqKit 2.8.2, SingleM 0.16.0, Sphinx-RTD-Theme 2.0.0, Stack 3.1.1, SuiteSparse 7.7.0, + SuperLU 6.0.1, SuperLU_DIST 8.2.1, scArches 0.6.1, scib-metrics 0.5.1, scvi-tools 1.1.2, sdsl-lite 2.0.3, + setuptools-rust 1.9.0, sirocco 2.1.0, slepc4py 3.20.2, smafa 0.8.0, snpEff 5.2c, spaCy 3.7.4, spektral 1.2.0, + spglib-python 2.5.0, spglib 2.5.0, TELEMAC-MASCARET 8p5r0, Tk 8.6.14, Tkinter 3.12.3, Trycycler 0.5.5, tiktoken 0.7.0, + timm 1.0.8, UCX-CUDA 1.16.0, unixODBC 2.3.12, utf8proc 2.9.0, VSEARCH 2.28.1, virtualenv 20.26.2, WRF 4.5.1, + Wayland 1.23.0, X11 20240607, XGBoost 2.1.1, XML-LibXML 2.0210, x264 20240513, x265 3.6, xarray 2024.5.0, xtb-IFF 1.1, + xtb 6.7.1, xtensor 0.24.7, yelp-xsl 42.1 +- minor enhancements, including: + - add internal CUDA header patch for PSM2 v12.0.1 (#20804) + - add patch for JupyterHub support to recent tensorboard easyconfigs (#20823) + - make sure that recent ImageMagick versions pick up the right pkgconf + improve sanity check for ImageMagick (#20900) + - also install utilities for recent versions of FUSE 3.x (#20918) + - add RISC-V support to x264 v20231019 (#20968) + - add RISC-v support to recent LAME easyconfigs by removing workaround for finding libncurses (#20970) + - enable PIC in recent x265 easyconfigs to solve compilation errors on RISC-V (#20971) + - add extensions to R-bundle-CRAN: missmDA (#21167, #21183). insight (#21260), performance + datwizard + bayestestR (#21272, #21285) + - add Qt support to VTK 9.3.0 (#21221) + - add `helper_scripts` to `$PATH` in easyconfig for ProteinMPNN v1.0.1-20230627 (#21289) + - also build & install the plugins with OpenFOAM v2406 (#21332) +- various bug fixes, including: + - fix easyconfigs for recent versions of QuantumESPRESSO (#20070) + - add wrapper for Julia with linking safeguards and delegate environment setup to JuliaPackage (#20103) + - fix typo in description of SuiteSparse v7.7.0 (#20567) + - add 'pic' flag to IML (#20789) + - add patch to recent SciPy-bundle easyconfigs to fix build error with numpy with some Fortran compilers (#20817) + - rename unpacked sources for components of EasyBuild v4.9.2, to ensure that '`--install-latest-eb-release`' works with older EasyBuild versions (#20818) + - fix build of OpenBLAS 0.3.24 on A64FX (#20820) + - remove maturin build dependency from langchain-antropic (#20825) + - add GMP and MPFR as dependencies to OpenFOAM v2306 and v2312 (#20841) + - add patch to SciPy-bundle 2024.05 that fixes numpy test failures on RISC-V (#20847) + - skip unreliable memory leak test in PyTorch 2.1.2 (#20874) + - use PyYAML 6.0.1 instead of 6.0 for recent ReFrame versions to fix problem with Cython 3.x (#20879) + - use PyPI source tarball and gfbf/2023a toolchain for pyBigWig (#20881) + - add fix for failing test on zen4 to Highway 1.0.4 (#20942) + - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#20949) + - only use libxsmm as dependency for CP2K 2023.1 w/ `foss/2023a` on x86_64 (#20951) + - copy missing `rsem_perl_utils.pm` in DETONATE, since it's required by `rsem-eval-calculate-score` command (#20956) + - set `$SATSUMA2_PATH` so Satsuma2 can locate executables (#20957) + - disable auto-vectorizer (`-ftree-vectorize`) for OpenFOAM v10 + v11 when using toolchain that with GCC >= 11 (#20958) + - disable test step for WIEN2k 23.2 because files required by it can no longer be downloaded (#20969) + - add patch to fix Qt6 issues with ParaView v5.12.0, e.g. representation selection (#21002) + - update homepage in phonopy easyconfigs (#21014) + - make libunwind dependency architecture specific in Extrae 4.2.0 easyconfig (#21017) + - add `OPENSSL_ENABLE_SHA1_SIGNATURES` for building `ansys-pythonnet` (#21028) + - fix download URLs for old Intel software (2018-2023) by using `IRC_NAS` instead of `irc_nas` (#21108) + - update source and homepage URLs in Szip easyconfigs (#21129) + - rename source URL in HDF v4.2.16-2 easyconfig (#21130) + - consistently fix homeage + source URL for `HDF` + `h4toh5` (#21134) + - ensure that recent BioPerl easyconfigs use `Bundle` easyblock (#21136) + - fix checksum checks for easyconfigs using a `Bundle`-like easyblock in easyconfigs test suite (#21143) + - add pkgconf build dependency to scikit-misc v0.3.1 (#21144) + - explicitly disable use of MySQL in recent GDAL easyconfigs (#21156) + - fix easyconfig tensorflow-probability v0.20.0 to pass `pip check` (#21172) + - stop RStudio-Server 2023.09 from installing R packages (+ move to `foss/2023a` toolchain) (#21175) + - remove `Time::HiRes` from `Perl-bundle-CPAN` since there's newer version in `Perl` (#21198) + - fix build of STAR 2.7.11a + 2.7.11b on non-x86 architectures by avoiding use of `-maxv2` + add missing `xxd` build dependency (#21200) + - add missing cairo dependency for python-igraph v0.10.6 (#21211) + - add patch for xtb 6.7.0 to fix build failure due to changes in tblite (#21255) + - add patch for HDF5 v1.14.3 to suppress fp exceptions (#21280) + - update easyconfig for dorado 0.7.3 to properly use provided OpenSSL dependency, and not install external libraries into its own lib directory (#21297) + - use proper Python dependency for OTF2 (#21325) + - use source tarballs from GitHub for recent libdap easyconfigs (#21334) + - remove Highway build dependency in Brunsli easyconfigs, since it's not actually required at all (#21366) + - add alternative checksum for bold 1.3.0 extension in R-bundle-CRAN (#21370) +- other changes: + - archive outdated example easyconfigs for Fujitsu toolchain (#20781) + - upgrade rpmrebuild build dependency to version 2.18 in bcl-convert 4.2.7 easyconfig (#20861) + - use proper dependency for Safetensors in easyconfig for Transformers v4.39.3 (#20864) + - remove CMake Arrow flag as there is no Arrow dependency in recent GDAL easyconfigs (#20905) + - whitelist `ConfigureMakePythonPackage` for `sanity_check_paths` CI check (#20963) + - rename `gubbins-2.4.0.eb` to `Gubbins-2.4.0.eb` (#20995) + - make pytest v7.4.2 independent of Python-bundle-PyPI (#21004) + - reorganize Flax/JAX stack in 2023a: move `jax` + `Optax` to `gfbf/2023a` toolchain + use standalone `Flax` + `absl-py` as dependencies (#21038) + - use stand-alone absl-py as dependency for jax w/ `gfbf/2023a` (#21039) + - remove Cython dependency from Python-bundle-PyPI 2024.06 + add standalone easyconfig for Cython 3.0.10 (#21233) + - add Cython build dependency for SciPy-bundle v2024.05 (#21235) + - use top-level parameters for `use_pip` & co instead of `exts_default_options` for `PythonBundle` easyconfigs (#21292) v4.9.2 (12 June 2024) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..2677e62fda1 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.4.0-GCC-12.3.0.eb @@ -0,0 +1,70 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# Thomas Eylenbosch - Gluo NV +# Update: Petr Král (INUITS) +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '1.4.0' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), + ('Term::ProgressBar', '2.23', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb new file mode 100644 index 00000000000..eb1a53ff8da --- /dev/null +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ALL' +version = '0.9.2' + +homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing' +description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic +domain-based load balancing into particle based simulation codes. The library +is developed in the Simulation Laboratory Molecular Systems of the Jülich +Supercomputing Centre at Forschungszentrum Jülich.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"] +sources = ['loadbalancing-v%(version)s.tar.gz'] +checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Boost', '1.83.0'), # only needed for tests +] + +dependencies = [ + ('VTK', '9.3.0'), +] + +configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' +configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod', + 'lib/libALL.a', 'lib/libALL_fortran.a' + ], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..c5c4c40ac5b --- /dev/null +++ b/easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb @@ -0,0 +1,51 @@ +easyblock = 'CmdCp' + +name = 'APOST3D' +version = '20240527' +local_commit = 'e06c8b0' + +description = """ +Open-source APOST-3D software features a large number of wavefunction analysis tools developed +over the past 20 years, aiming at connecting classical chemical concepts with the electronic +structure of molecules. APOST-3D relies on the identification of the atom in the molecule +(AIM), and several analysis tools are implemented in the most general way so that they can be +used in combination with any chosen AIM. +A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators. +""" +homepage = 'https://github.com/mgimferrer/APOST3D' + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +builddependencies = [ + ('make', '4.4.1'), +] + +source_urls = ['https://github.com/mgimferrer/APOST3D/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] + +local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' +# Compile provided Libxc version 4.2.3 +# (it is not possible to couple APOST-3D with newer Libxc libraries): +local_cmds += 'bash compile_libxc.sh && ' +# Compile +local_cmds += 'make -f Makefile_profgen && ' +# Run test calculations on single-processor: +local_cmds += 'bash compiler-runtest && ' +# Recompile using info geneated in previous step +local_cmds += 'make -f Makefile_profuse && ' +# Run test calculations in parallel: +local_cmds += 'bash compiler-runtest2' + +cmds_map = [('.*', local_cmds)] + +local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom'] + +files_to_copy = [(local_bin_files, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': [''], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc5f92c2b70 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.3' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('APR', '1.7.4'), + ('SQLite', '3.45.3'), + ('expat', '2.6.2'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ac5ed02a98 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.4' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..506079ce98c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..2c31ade2eb0 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb @@ -0,0 +1,74 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('GSL', '2.7'), + ('SAMtools', '1.18'), + ('HTSlib', '1.18'), # also provides tabix + ('BCFtools', '1.18'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '7.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.42.0'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..24951c68814 --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240722.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20240722.0' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['f50e5ac311a81382da7fa75b97310e4b9006474f9560ac46f54a9967f07d4ae3'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = "-DABSL_PROPAGATE_CXX_STD=ON " + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['lib/libabsl_base.' + SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 24ce3fe1c31..2e121781a46 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index a9f9a888154..7b025287362 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb index 6a0d2fa4ece..cbcdab88d6e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update5.eb @@ -10,7 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15825/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15825/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['3f203ee63df37e87423fdd4cbeb5ec027b3d11e50c9121935f8b323dd635e866'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb index 2a7de357e47..144362e2eb7 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17730/'] sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh'] checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb index 55354cc6e25..ec07e00e07e 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18220/'] sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh'] checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb index 58235ccff90..34a2115a37c 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb @@ -13,7 +13,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18730/'] sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh'] checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb index 187fcafa180..e6d811a03a0 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb @@ -11,7 +11,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = SYSTEM source_urls = [ - 'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/'] + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19094/'] sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh'] checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d'] diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch new file mode 100644 index 00000000000..34994664f80 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch @@ -0,0 +1,13 @@ +fix import of protein_letters_3to1 from Biopython +author: Kenneth Hoste (HPC-UGent) +--- AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py.orig 2024-06-05 09:30:16.114746286 +0200 ++++ AlphaPulldown/alphapulldown/utils/remove_clashes_low_plddt.py 2024-06-05 09:30:35.242665615 +0200 +@@ -4,7 +4,7 @@ + from alphafold.data.mmcif_parsing import parse + from alphafold.common.residue_constants import residue_atoms, atom_types + from Bio.PDB import NeighborSearch, PDBIO, MMCIFIO +-from Bio.PDB.Polypeptide import protein_letters_3to1 ++from Bio.Data.SCOPData import protein_letters_3to1 + from Bio import SeqIO + from colabfold.batch import convert_pdb_to_mmcif + from Bio.PDB import Structure, Model, Chain, Residue diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..492a787c919 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,106 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25', versionsuffix), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb new file mode 100644 index 00000000000..f410c438e23 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-2.0.0b4-foss-2022a.eb @@ -0,0 +1,104 @@ +# created by Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'AlphaPulldown' +version = '2.0.0b4' + +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('OpenMM', '8.0.0'), + ('Kalign', '3.3.5'), + ('PyYAML', '6.0'), + ('jax', '0.3.25'), # also provides absl-py + ('Biopython', '1.79'), + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('TensorFlow', '2.11.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('dm-tree', '0.1.8'), + ('py3Dmol', '2.0.1.post1'), + ('HMMER', '3.3.2'), + ('HH-suite', '3.3.0'), + ('Uni-Core', '0.0.3'), +] + +use_pip = True + +exts_list = [ + ('importlib-resources', '5.13.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['82d5c6cca930697dbbd86c93333bb2c2e72861d4789a11c2662b933e5ad2b528'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('ihm', '1.3', { + 'checksums': ['09f69809fd81509cc26b60253c55b02ce79fc01fc8f4a068bca2953a7dfd33be'], + }), + ('modelcif', '1.0', { + 'checksums': ['e8375bc502a73dcfab0b7fbdd454d67d393bbb8969981eb52199d77192a3de56'], + }), + (name, version, { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/KosinskiLab', + 'repo_name': 'AlphaPulldown', + 'tag': version, + 'recursive': True, + }, + }], + 'patches': ['AlphaPulldown-2.0.0b2_fix-import-protein_letters_3to1.patch'], + 'checksums': [ + None, + 'd41247cd12f6ef8579adbc893f6c1af5fba051167ee838449974365f4bdccf06', + ], + # remove strict version requirements for Python dependencies + 'preinstallopts': "sed -i 's/[>=]=.*//g' setup.cfg && ", + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], +} + +sanity_check_commands = [ + "run_multimer_jobs.py --help | grep 'A script to perform structure prediction'", + "convert_to_modelcif.py --help | grep 'turn it into a ModelCIF'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb index 85715fef495..0c588b9f16b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb index 87862215507..5219bd9c54f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-16.1.0-gfbf-2023b.eb @@ -39,10 +39,10 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_ORC=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " -configopts += "-DZSTD_ROOT=$EBROOTZSTD " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DARROW_WITH_ZSTD=ON -DZSTD_ROOT=$EBROOTZSTD " # install Python bindings _pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " @@ -52,7 +52,7 @@ _pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " _pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " _pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " _pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 PYARROW_WITH_ORC=1 " exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -81,6 +81,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'import pyarrow.orc'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..73e0608725b --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2023.02.20' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('makeinfo', '7.0.3'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..faadde2a51d --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7f6d595a7c5 --- /dev/null +++ b/easybuild/easyconfigs/a/accelerate/accelerate-0.33.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'accelerate' +version = '0.33.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/huggingface/accelerate' +description = """A simple way to launch, train, and use PyTorch models on almost any device and +distributed configuration, automatic mixed precision (including fp8), +and easy-to-configure FSDP and DeepSpeed support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('Safetensors', '0.4.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.24.5', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'], + }), +] + +sanity_check_commands = ['accelerate test'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb new file mode 100644 index 00000000000..4c13c121047 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fd05a43146f --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.40')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4333348a741 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.11-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.11' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9f3f2f69b995f9ad37359072fbc69a3a88bfba081fc83e9be30e14662795bb4d'] + +dependencies = [('binutils', '2.42')] + +configopts = ['--disable-shared --enable-static', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT, 'lib64/libasound.a'], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a4f3a288e9 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['eabbae22f315d24cc2ce786a092478ec8e245208c9877fb213c2172a6ecb9302'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fcd6d723f16 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.2' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['39bf67452fa41d0948c2197601053f48b3d78a029389734332a6309a680c6c87'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +sanity_check_commands = ["getfattr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9b70b1a9008 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.17.54' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), # required for awscrt +] + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('ruamel.yaml', '0.18.6'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'], + }), + ('botocore', '1.35.22', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'], + }), + ('s3transfer', '0.10.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'], + }), + ('prompt_toolkit', '3.0.47', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'], + }), + ('distro', '1.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'], + }), + ('awscrt', '0.21.5', { + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + 'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'], + }), + # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'` + # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550 + ('urllib3', '1.26.20', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'], + }), + (name, version, { + # version requirements are too strict + 'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch new file mode 100644 index 00000000000..83f35651997 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/3rd-party-removal.patch @@ -0,0 +1,176 @@ +Removal of sqlite3, boost and zstd from 3-party modules +Author: J. Sassmannshausen +diff --git a/bgen.tgz.orig/3rd_party/wscript b/bgen.tgz/3rd_party/wscript +index 220728a..e69de29 100644 +--- a/bgen.tgz.orig/3rd_party/wscript ++++ b/bgen.tgz/3rd_party/wscript +@@ -1,2 +0,0 @@ +-def build( bld ): +- bld.recurse( [ 'boost_1_55_0', 'sqlite3', 'zstd-1.1.0' ] ) +diff --git a/bgen.tgz.orig/Makefile b/bgen.tgz/Makefile +index a7b0ac8..c62ac16 100644 +--- a/bgen.tgz.orig/Makefile ++++ b/bgen.tgz/Makefile +@@ -1,14 +1,9 @@ + FLAGS = -g -std=c++11 -lz \ + -I genfile/include \ + -I db/include \ +--I 3rd_party/boost_1_55_0 \ +--I 3rd_party/zstd-1.1.0 \ +--I 3rd_party/zstd-1.1.0/lib \ +--I 3rd_party/zstd-1.1.0/lib/common \ +--I 3rd_party/zstd-1.1.0/lib/compress \ +--I 3rd_party/zstd-1.1.0/lib/decompress \ +--I 3rd_party/sqlite3 \ +--I include/3rd_party/sqlite3 \ ++-I ${EBBOST}/include \ ++-I ${EBDEVELZSTD}/include \ ++-I ${EBSQLITE3}/include \ + -D SQLITE_ENABLE_COLUMN_METADATA \ + -D SQLITE_ENABLE_STAT4 \ + -D SQLITE_MAX_EXPR_DEPTH=10000 \ +diff --git a/bgen.tgz.orig/db/include/db/SQLStatement.hpp b/bgen.tgz/db/include/db/SQLStatement.hpp +index e107bd2..fca5957 100644 +--- a/bgen.tgz.orig/db/include/db/SQLStatement.hpp ++++ b/bgen.tgz/db/include/db/SQLStatement.hpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp b/bgen.tgz/db/include/db/SQLite3Connection.hpp +index b4bd219..cfbbd3a 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Connection.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Connection.hpp +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/Connection.hpp" + #include "db/Transaction.hpp" + #include "db/Error.hpp" +diff --git a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp b/bgen.tgz/db/include/db/SQLite3Statement.hpp +index d41a710..76dbfb6 100644 +--- a/bgen.tgz.orig/db/include/db/SQLite3Statement.hpp ++++ b/bgen.tgz/db/include/db/SQLite3Statement.hpp +@@ -11,7 +11,7 @@ + #include + #include + +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + +diff --git a/bgen.tgz.orig/db/src/SQLStatement.cpp b/bgen.tgz/db/src/SQLStatement.cpp +index 60168c6..32576ca 100644 +--- a/bgen.tgz.orig/db/src/SQLStatement.cpp ++++ b/bgen.tgz/db/src/SQLStatement.cpp +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLStatement.hpp" + + namespace db { +diff --git a/bgen.tgz.orig/db/src/SQLite3Statement.cpp b/bgen.tgz/db/src/SQLite3Statement.cpp +index 84e0658..03b3d5e 100644 +--- a/bgen.tgz.orig/db/src/SQLite3Statement.cpp ++++ b/bgen.tgz/db/src/SQLite3Statement.cpp +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "sqlite3/sqlite3.h" ++#include "sqlite3.h" + #include "db/SQLite3Connection.hpp" + #include "db/SQLStatement.hpp" + #include "db/SQLite3Statement.hpp" +diff --git a/bgen.tgz.orig/db/wscript b/bgen.tgz/db/wscript +index 7b0b617..a3861f0 100644 +--- a/bgen.tgz.orig/db/wscript ++++ b/bgen.tgz/db/wscript +@@ -5,8 +5,8 @@ def build( bld ): + bld.stlib( + target = 'db', + source = sources, +- includes='./include', ++ includes='${EBSQLITE}/include ./include', + cxxflags = [], + use = 'boost sqlite3', +- export_includes = './include' ++ export_includes = '${EBSQLITE}/include ./include' + ) +diff --git a/bgen.tgz.orig/wscript b/bgen.tgz/wscript +index a6385d9..47b9fc9 100644 +--- a/bgen.tgz.orig/wscript ++++ b/bgen.tgz/wscript +@@ -63,7 +63,7 @@ def build( bld ): + use = 'zlib zstd sqlite3 db', + export_includes = 'genfile/include' + ) +- bld.recurse( [ '3rd_party', 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) ++ bld.recurse( [ 'appcontext', 'genfile', 'db', 'apps', 'example', 'test', 'R' ] ) + # Copy files into rbgen package directory + for source in bgen_sources: + bld( rule = 'cp ${SRC} ${TGT}', source = source, target = 'R/rbgen/src/bgen/' + os.path.basename( source.abspath() ), always = True ) +@@ -126,12 +126,12 @@ class ReleaseBuilder: + shutil.copytree( 'R/package/', rbgen_dir ) + os.makedirs( os.path.join( rbgen_dir, "src", "include" )) + os.makedirs( os.path.join( rbgen_dir, "src", "include", "boost" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "include", "zstd" )) + os.makedirs( os.path.join( rbgen_dir, "src", "db" )) + os.makedirs( os.path.join( rbgen_dir, "src", "bgen" )) + os.makedirs( os.path.join( rbgen_dir, "src", "boost" )) + os.makedirs( os.path.join( rbgen_dir, "src", "sqlite3" )) +- os.makedirs( os.path.join( rbgen_dir, "src", "zstd-1.1.0" )) ++ os.makedirs( os.path.join( rbgen_dir, "src", "zstd" )) + + # Copy source files in + from glob import glob +@@ -141,11 +141,11 @@ class ReleaseBuilder: + for filename in glob( 'db/src/*.cpp' ): + shutil.copy( filename, os.path.join( rbgen_dir, "src", "db", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/sqlite3/sqlite3/sqlite3.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "sqlite3", os.path.basename( filename ) ) ) + +- for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) ++# for filename in glob( '3rd_party/zstd-1.1.0/lib/common/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/compress/*.c' ) + glob( '3rd_party/zstd-1.1.0/lib/decompress/*.c' ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "zstd-1.1.0", os.path.basename( filename ) ) ) + + boostGlobs = [ + 'libs/system/src/*.cpp', +@@ -160,14 +160,14 @@ class ReleaseBuilder: + 'libs/chrono/src/*.cpp', + ] + +- for pattern in boostGlobs: +- for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): +- shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) ++# for pattern in boostGlobs: ++# for filename in glob( '3rd_party/boost_1_55_0/%s' % pattern ): ++# shutil.copy( filename, os.path.join( rbgen_dir, "src", "boost", os.path.basename( filename ) ) ) + + include_paths = [ +- "3rd_party/boost_1_55_0/boost/", +- "3rd_party/zstd-1.1.0/", +- "3rd_party/sqlite3/", ++ "${EBBOOST}", ++ "${EBROOTZSTD}", ++ "${EBROOTSQLITE}", + "genfile/include/genfile", + "db/include/db" + ] diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..b0c0bc1be02 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-11.2.0.eb @@ -0,0 +1,74 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch new file mode 100644 index 00000000000..5d7c0e471c3 --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre_streampos.patch @@ -0,0 +1,12 @@ +diff -ruN 1.1.7.tgz.orig/src/View.cpp 1.1.7.tgz/src/View.cpp +--- 1.1.7.tgz.orig/src/View.cpp 2020-06-29 01:19:43.000000000 -0700 ++++ 1.1.7.tgz/src/View.cpp 2022-06-06 18:05:10.650577000 -0700 +@@ -177,7 +177,7 @@ + + // get file size + { +- std::ios::streampos origin = m_stream->tellg() ; ++ std::streampos origin = m_stream->tellg() ; + m_stream->seekg( 0, std::ios::end ) ; + m_file_metadata.size = m_stream->tellg() - origin ; + m_stream->seekg( 0, std::ios::beg ) ; diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb new file mode 100644 index 00000000000..50bbeea16ee --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'BRiAl' +version = '1.2.12' + +homepage = 'https://github.com/BRiAl/BRiAl' +description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.83.0'), + ('m4ri', '20200125'), + ('CUDD', '3.0.0'), +] + +configopts = "--with-boost=$EBROOTBOOST " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..acdc093c96d --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Qt5', '5.15.10')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..2e20ceba904 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesOpt/BayesOpt-0.9-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'BayesOpt' +version = '0.9' + +homepage = 'https://rmcantin.github.io/bayesopt' +description = """BayesOpt is an efficient implementation of the Bayesian optimization methodology for +nonlinear-optimization, experimental design, stochastic bandits and hyperparameter tunning""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rmcantin/bayesopt/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4e60cfac380eccd2d1adc805b752b5bd22a1d8a27dc6aeb630c403adc04f28c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('NLopt', '2.7.1'), +] + +# don't build included version of NLopt (use provided dependency) +configopts = "-DNLOPT_BUILD=OFF" + +sanity_check_paths = { + 'files': ['lib/libbayesopt.a'], + 'dirs': ['include/bayesopt'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb new file mode 100644 index 00000000000..541dedf129e --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-4.1.2-Linux.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# Updated by +# Author: Alex Salois +# Research Cyberinfrastructure +# Montana State University + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '4.1.2' +versionsuffix = '-Linux' + +homepage = 'https://www.evolution.reading.ac.uk/SoftwareMain.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = SYSTEM + +source_urls = ['https://www.evolution.reading.ac.uk/BayesTraitsV%(version)s/Files/'] +sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['d5251c2b256405fc63c55caf8371b267530a3c4ebd11cbfd3ebd4013c9d49db0'] + +sanity_check_paths = { + 'files': ['BayesTraitsV4', 'Artiodactyl.trees', 'Bird.trees', 'Mammal.trees', + 'Marsupials.trees', 'NortheastBantu.trees', 'Primates.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95cb6cf3228 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.12.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.5', { + 'checksums': ['5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb new file mode 100644 index 00000000000..59f7c1a7cd5 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.9' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'BiG-SCAPE-1.1.5_use_env_var_for_html.patch', + 'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch', +] +checksums = [ + {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Biopython', '1.84'), + ('scikit-learn', '1.4.0'), + ('networkx', '3.2.1'), + ('HMMER', '3.4'), + ('FastTree', '2.1.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'bigscape'} + +local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape' + +sanity_check_paths = { + 'files': ['bin/bigscape'], + 'dirs': [local_lib_py_bigscape_path], +} + +sanity_check_commands = [ + 'bigscape --help', +] + +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path, +} + +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 8caddd5df22..e8e52099b07 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb index b47216124f8..4212570abb1 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -5,7 +5,7 @@ # Fred Hutchinson Cancer Research Center # Thomas Eylenbosch - Gluo NV -easyblock = 'PerlModule' +easyblock = 'Bundle' name = 'BioPerl' version = '1.7.8' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ba3029a6a41 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb new file mode 100644 index 00000000000..8d4385e45f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Biotite' +version = '0.41.0' + +homepage = 'https://www.biotite-python.org/' +description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to +identify homologous sequence regions in a protein family or you would like to +find disulfide bonds in a protein structure: Biotite has the right tool for +you. This package bundles popular tasks in computational molecular biology into +a uniform Python library.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), +] + +use_pip = True + +exts_list = [ + ('biotite', version, { + 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..427ebbbe2b7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-14.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.42', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..1814c8648e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index 22f38cbf5f9..9e505b4df5e 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb index 301194a32a4..0661abf0609 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb index 7522f1025e3..57bba400bde 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb index cc914cae6cd..df29a7bda20 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.3'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb index 22917f651e9..42e15bb4356 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.0.9'), - ('Highway', '1.0.4'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb index 249b1170411..6481ba231cd 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb @@ -22,7 +22,6 @@ builddependencies = [ dependencies = [ ('Brotli', '1.1.0'), - ('Highway', '1.0.7'), ] # skip use of third_party directory, since we provide Brotli via a proper dependency diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3afc7fffd75 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('Brotli', '1.1.0'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/\\(brotli...\\)-static/\\1/g' ../brunsli-%(version)s/brunsli.cmake && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb new file mode 100644 index 00000000000..8215f2c822a --- /dev/null +++ b/easybuild/easyconfigs/b/bayesian-optimization/bayesian-optimization-1.5.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bayesian-optimization' +version = '1.5.1' + +homepage = 'https://bayesian-optimization.github.io/BayesianOptimization/index.html' +description = "Pure Python implementation of bayesian global optimization with gaussian processes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorama', '0.4.6', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6'], + }), + ('bayesian_optimization', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'modulename': 'bayes_opt', + 'checksums': ['098946c933d6039073b7ccb0c9f1b4c73ac6e39350043b02e5243b08583c4c5c'], + }), +] + +sanity_check_commands = ["python -c 'from bayes_opt import BayesianOptimization'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..2c2bbf6705b --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('CUDA', '12.1.1', '', SYSTEM), +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_CUDA=ON ' + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..94b762d7803 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.42-GCCcore-14.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.42' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5d2a6c1d49686a557869caae08b6c2e83699775efd27505e01b2f4db1a024ffc'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.3.1'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8127a86c558 --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), +] + +configopts = '-DCOMPUTE_BACKEND=cuda' +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cuda121.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb new file mode 100644 index 00000000000..8b360bb263b --- /dev/null +++ b/easybuild/easyconfigs/b/bitsandbytes/bitsandbytes-0.43.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'bitsandbytes' +version = '0.43.3' + +homepage = 'https://huggingface.co/docs/bitsandbytes/main/en/index' +description = "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch." +github_account = 'bitsandbytes-foundation' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a468bc977da19c176cc578954bfd7a3c64182f387a6849e9f0a38d5cba1b4df'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('SciPy-bundle', '2023.07'), +] + +skipsteps = ['install'] + +postinstallcmds = [ + 'pip install --prefix=%(installdir)s --no-deps --ignore-installed --no-index --no-build-isolation %(start_dir)s', +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/bitsandbytes/libbitsandbytes_cpu.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import bitsandbytes'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb new file mode 100644 index 00000000000..ec9a99bc306 --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'bliss' +version = '0.77' + +homepage = 'https://users.aalto.fi/~tjunttil/bliss/' +description = """Bliss is an open-source tool for computing canonical labelings and automorphism groups of graphs.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://users.aalto.fi/~tjunttil/bliss/downloads/'] +sources = [SOURCE_ZIP] +patches = ['bliss-0.77_install_fix.patch'] +checksums = [ + {'bliss-0.77.zip': 'acc8b98034f30fad24c897f365abd866c13d9f1bb207e398d0caf136875972a4'}, + {'bliss-0.77_install_fix.patch': '1550b6c7f8208f56093c0b6bf0d2e3df42afab81cd69eb70303515c9923e9513'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = "-DUSE_GMP=ON " + +sanity_check_paths = { + 'files': [ + 'bin/bliss', + 'lib/libbliss.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + ], +} + +sanity_check_commands = ["bliss -help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch new file mode 100644 index 00000000000..faea2ad4daf --- /dev/null +++ b/easybuild/easyconfigs/b/bliss/bliss-0.77_install_fix.patch @@ -0,0 +1,33 @@ +Adds install commands to CMakeLists.txt +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/bliss/-/blob/0.77-3/make-install.patch +diff -u CMakeLists.txt.orig CMakeLists.txt +--- CMakeLists.txt.orig 2021-02-18 11:59:34.000000000 +0100 ++++ CMakeLists.txt 2024-08-15 15:04:21.293765655 +0200 +@@ -62,3 +62,27 @@ + target_link_libraries(bliss-executable ${GMP_LIBRARIES}) + endif(USE_GMP) + set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss) ++ ++include(GNUInstallDirs) ++ ++set( ++ BLISS_HEADERS ++ src/bliss_C.h ++ src/uintseqhash.hh ++ src/abstractgraph.hh ++ src/stats.hh ++ src/digraph.hh ++ src/defs.hh ++ src/heap.hh ++ src/graph.hh ++ src/partition.hh ++ src/kqueue.hh ++ src/utils.hh ++ src/orbit.hh ++ src/timer.hh ++ src/bignum.hh ++) ++ ++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss) diff --git a/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fa57e4306e6 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-2.0.20240109-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '2.0.20240109' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://invisible-island.net/archives/byacc/'] +sources = ['byacc-%s.tgz' % version.split('.')[2]] +checksums = ['f2897779017189f1a94757705ef6f6e15dc9208ef079eea7f28abec577e08446'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb new file mode 100644 index 00000000000..af659719245 --- /dev/null +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'CAMPARI' +version = '4.0' +_date = '12202020' + +homepage = 'http://campari.sourceforge.net/V4/index.html' +description = """ +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological +relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte +Carlo and molecular dynamics in seamless fashion.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] +checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.1'), + ('libtirpc', '1.3.3'), +] + +start_dir = 'source' + +# remove hardcoded paths in configure script +preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' +# ignore default compiler settings and use EB build environment +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags +configopts += '--enable-mpi=auto ' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' + +buildopts = 'all' + +maxparallel = 10 + +postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] + +_binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] +_libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], + 'dirs': [], +} + +sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb index 203b4e4cd9f..743bf47a462 100644 --- a/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb +++ b/easybuild/easyconfigs/c/CAMPARI/CAMPARI-4.0-intel-2023a.eb @@ -30,9 +30,10 @@ start_dir = 'source' # remove hardcoded paths in configure script preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' # ignore default compiler settings and use EB build environment -configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="$FCFLAGS" ' +local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' +configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags configopts += '--enable-mpi=auto ' -configopts += 'LIBS="$LIBS $LIBFFT -ltirpc"' +configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' buildopts = 'all' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..bd59609605c --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1a0cf57158 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-13.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.), Pavel Tománek (Inuits) +# Update: Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.38.0'), + ('zlib', '1.2.13'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb new file mode 100644 index 00000000000..58cf406d164 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.3.0-iimpi-2022a.eb @@ -0,0 +1,58 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.3.0' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29019/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10c878227baf718a6917837527d4426c2d0022cfac4457c65155b9c57f091f6b'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb new file mode 100644 index 00000000000..1144c2b34cc --- /dev/null +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'CESM-deps' +version = '2' + +homepage = 'https://www.cesm.ucar.edu/models/cesm2/' +description = """CESM is a fully-coupled, community, global climate model that +provides state-of-the-art computer simulations of the Earth's past, present, +and future climate states.""" + +# The following environment is suitable for CESM >= 2.2.2 and CTSM >= 5.2.0 +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('Perl', '5.36.1'), + ('XML-LibXML', '2.0209'), + ('ESMF', '8.6.0'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('netCDF-C++4', '4.3.1'), + ('PnetCDF', '1.12.3'), + ('git', '2.41.0', '-nodocs'), + ('git-lfs', '3.5.1', '', SYSTEM), +] + +components = [ + # install extra configuration tools and files for VSC clusters + ('cesm-config', '1.7.0', { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['c5aeb50595ca4d342a5024d593c2549acf16e72dadc5f39d9a7915d3dc8f3c13'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'], + 'dirs': ['machines', 'irods'], +} + +usage = """Environment to build and run CESM v2 simulations + 1. Download a release of CESM v2: `git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2` + 2. Add external programs for CESM: `cd cesm-2.2.2; ./manage_externals/checkout_externals` + 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/` + 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`""" + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..eaa1b0866ac --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.4.1' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.4.1.tar.gz': '66a1dc3f21800f9eeabd9eac577b91fcdd9aabba678fbba3b8527319110d1d25'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] +# curl for HTTPs support +dependencies = [ + ('cURL', '8.7.1'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = "&& make shared && make testprog" + + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['cd %(installdir)s/share && testprog'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..01aa21c6311 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' +name = 'CGAL' +version = '5.6.1' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['cdb15e7ee31e0663589d3107a79988a37b7b1719df3d24f2058545d1bcdd5837'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb new file mode 100644 index 00000000000..e1ce2f2a9e1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLANS/CLANS-2.0.8-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'CLANS' +version = '2.0.8' + +homepage = 'https://github.com/inbalpaz/CLANS' +description = """ +CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on +their sequence similarities. CLANS visualizes the dynamic clustering process and enables the +user to interactively control it and explore the cluster map in various ways. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('VisPy', '0.12.2'), + ('Biopython', '1.83'), + ('Pillow', '10.0.0'), + ('PyQt5', '5.15.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/inbalpaz/CLANS/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7b856ec3b13c420dbe30169e8cdd7d6899acb79042ca66920eafd05adf4d2815'], + }), +] + +sanity_check_commands = ['python -m clans -h'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..4bf02eab9a1 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.7.1-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.7.1' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['1c8304a7772ac6b99195f1300378c6e3ddf4ad07c85d64a04505652abb8a55f9'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb new file mode 100644 index 00000000000..3b42e01a2be --- /dev/null +++ b/easybuild/easyconfigs/c/CLUMPP/CLUMPP-1.1.2-Linux64.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'CLUMPP' +version = '1.1.2' +versionsuffix = '-Linux64' + +homepage = 'https://rosenberglab.stanford.edu/clumpp.html' +description = """ +CLUMPP is a program that deals with label switching and multimodality problems +in population-genetic cluster analyses.""" + +toolchain = SYSTEM + +source_urls = ['https://rosenberglab.stanford.edu/software/'] +sources = ['%(name)s_Linux64.%(version)s.tar.gz'] +checksums = ['58cf3fe9e37f890621a76a244362256ffe4dde5e409346ae811d56af26cfe724'] + +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && mv CLUMPP bin/' +] + +sanity_check_paths = { + 'files': ['bin/CLUMPP'], + 'dirs': [], +} + +_clumpp_test_cmd = [ + "tmpdir=$(mktemp -d)", + "cp %(installdir)s/{paramfile,arabid.popfile,arabid.permutationfile} $tmpdir", + "cd $tmpdir", + "CLUMPP", +] + +sanity_check_commands = [ + " && ".join(_clumpp_test_cmd), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb new file mode 100644 index 00000000000..c6f619d9d75 --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = "ConfigureMake" + +name = 'CORSIKA' +version = '77550' + +homepage = "https://www.iap.kit.edu/corsika" +description = """CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed +simulation of extensive air showers initiated by high energy cosmic ray +particles. Protons, light nuclei up to iron, photons, and many other particles +may be treated as primaries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +download_instructions = "Sources have to be requested to the developers" +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_include.patch'] +checksums = [ + {'corsika-77550.tar.gz': 'fed74c144e22deb5a7c1d2dc1f04f0100eb2732cb48665a3da49ce471a3775ee'}, + {'CORSIKA-77550_fix_include.patch': 'e858fc4c1fa33d31d050b2fca50e130c23b2d3e4b81b851af34dc3f39e9c709e'}, +] + +dependencies = [ + ("ROOT", "6.30.06"), +] + +# custom coconut script does not recognize -j +parallel = False + +# execute ./coconut manually with your own options and extract configure command from top of config.log +_mpi_opts = "--enable-PARALLEL --with-mpirunner-lib=src/parallel --enable-PARALLELIB " +configopts = "CORDETECTOR=HORIZONTAL CORTIMELIB=TIMEAUTO CORHEMODEL=QGSJETII CORLEMODEL=URQMD " +configopts += "--enable-UPWARD --enable-SLANT --enable-THIN --enable-COREAS " +configopts += _mpi_opts + +build_cmd = "./coconut" +buildopts = "--batch " + _mpi_opts + +install_cmd = ' && '.join([ + 'mkdir -p %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/run/* %(installdir)s/bin/', +]) + +sanity_check_paths = { + 'files': ['bin/mpi_corsika77550Linux_QGSII_urqmd_thin_coreas_parallel_runner'], + 'dirs': [], +} + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch new file mode 100644 index 00000000000..e7bc3863fae --- /dev/null +++ b/easybuild/easyconfigs/c/CORSIKA/CORSIKA-77550_fix_include.patch @@ -0,0 +1,22 @@ +Move include out of function to avoid error: +/usr/include/sys/stat.h:453:1: error: nested function ‘stat’ declared ‘extern’ +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -Nur corsika-77550.orig/src/parallel/mpi_runner.c corsika-77550/src/parallel/mpi_runner.c +--- corsika-77550.orig/src/parallel/mpi_runner.c 2024-04-18 18:30:39.000000000 +0200 ++++ corsika-77550/src/parallel/mpi_runner.c 2024-08-09 16:15:39.969688000 +0200 +@@ -99,6 +99,7 @@ + #include + #include + #include "config.h" ++#include + + /////////////////////initializing parameters/////////////////// + //the number of data type block in the MPI message +@@ -1023,7 +1024,6 @@ + strcpy(str2, strtmp); + } + strcpy(statdir,str2); +- #include + struct stat sb; + if (stat(statdir, &sb) == 0 && S_ISDIR(sb.st_mode)) + { diff --git a/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb new file mode 100644 index 00000000000..0f347ce481e --- /dev/null +++ b/easybuild/easyconfigs/c/COSTA/COSTA-2.2.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'COSTA' +version = '2.2.2' + +homepage = 'https://github.com/eth-cscs/COSTA' +description = """OSTA is a communication-optimal, highly-optimised algorithm for data redistribution +accross multiple processors, using MPI and OpenMP and offering the possibility +to transpose and scale some or all data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/COSTA/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcosta.a'], + 'dirs': ['include/costa'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb similarity index 59% rename from easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb rename to easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb index 7649571fc62..87ae95876bf 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-20240319-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023b.eb @@ -5,8 +5,7 @@ easyblock = 'CMakeMake' name = 'CREST' -version = '20240319' -_commit = '2719412edf8bb606cebdd4cd6bbb4cdbd249e1e5' +version = '2.12' homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' description = """CREST is an utility/driver program for the xtb program. Originally it was designed @@ -16,23 +15,24 @@ description = """CREST is an utility/driver program for the xtb program. Origina program) and tool for the creation and analysation of structure ensembles. """ -toolchain = {'name': 'gfbf', 'version': '2023a'} -toolchainopts = {'opt': True, 'optarch': True, 'extra_fflags': '-ffree-line-length-none'} - -separate_build_dir = False +toolchain = {'name': 'gfbf', 'version': '2023b'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['770b7ca72bc47bc4e1ffd8ca56566df7b03f4d3b702b04ec6b83bad9a125884d'] +sources = ['v%(version)s.tar.gz'] +patches = ['CREST-2.12-longline.patch'] +checksums = [ + {'v2.12.tar.gz': '390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'}, + {'CREST-2.12-longline.patch': '596ca2bcce3bbdfe99a3849934f41b388fb763a4898240091593b9b6a454fea9'}, +] -builddependencies = [('CMake', '3.26.3')] +builddependencies = [('CMake', '3.27.6')] -dependencies = [('xtb', '6.6.1')] # required to run the program +dependencies = [('xtb', '6.7.1')] # required to run the program # Simple test command just to check if the program is working: -test_cmd = 'export PATH=%%(builddir)s/%%(namelower)s-%s:$PATH && ' % _commit -test_cmd += 'cd %%(builddir)s/%%(namelower)s-%s/examples/expl-0/ && ./run.sh ' % _commit +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' sanity_check_paths = { 'files': ['bin/%s' % name.lower()], diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch new file mode 100644 index 00000000000..c3b84785f5f --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-longline.patch @@ -0,0 +1,16 @@ +Dealing with a long line, which gfortran does not like +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/crest-2.12.orig/src/qcg/solvtool.f90 b/crest-2.12/src/qcg/solvtool.f90 +index cec514c..f38b576 100644 +--- a/crest-2.12.orig/src/qcg/solvtool.f90 ++++ b/crest-2.12/src/qcg/solvtool.f90 +@@ -3158,7 +3158,8 @@ subroutine check_prog_path_iff(env) + str=trim(str) + open(unit=27, file=str, iostat=ios) + read(27,'(a)',iostat=ios) path +- if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' ++ if(ios .ne. 0) error stop 'No xtb-IFF found. This is currently required for QCG and available at & ++ https:/github.com/grimme-lab/xtbiff/releases/tag/v1.1' + + end subroutine check_prog_path_iff + diff --git a/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb new file mode 100644 index 00000000000..38fc051e0fb --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-3.0.2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CREST' +version = '3.0.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/crest-lab', + 'repo_name': 'crest', + 'tag': 'v%s' % version, + 'recursive': True, + }, +}] +checksums = [None] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('dftd4', '3.7.0'), + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), + ('xtb', '6.6.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index b71d2bfad4d..ad7b6aba80b 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] +patches = ['cuda-samples-11.3_multiple-sms.patch'] +checksums = [ + {'v11.3.tar.gz': '2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'}, + {'cuda-samples-11.3_multiple-sms.patch': 'b31613f4160456f0d0abf82999c7fb7eee781f0efadc8b9bbb5a02ef0f37e21d'}, +] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), @@ -32,7 +36,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb index d4240930bd1..ea78eae4061 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.6.tar.gz': '75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), @@ -33,7 +37,7 @@ local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..be16c76f3be --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '11.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v11.8.tar.gz': '1bc02c0ca42a323f3c7a05b5682eae703681a91e95b135bfe81f848b2d6a2c51'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 3e7ffe79da0..5a886ca74d4 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.1.tar.gz': 'f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), @@ -58,7 +62,7 @@ if ARCH == 'aarch64': local_filters += "Samples/3_CUDA_Features/cdpQuadtree/Makefile " local_filters += "Samples/3_CUDA_Features/cdpAdvancedQuicksort/Makefile " -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters # Remove libraries in the bin dir after a successful 'make' buildopts += " && rm bin/*/linux/release/lib*.so.*" diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb new file mode 100644 index 00000000000..89e1c6fc87b --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.2-GCC-11.3.0-CUDA-12.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '12.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['cuda-samples-11.6_multiple-sms.patch'] +checksums = [ + {'v12.2.tar.gz': '1823cfe28e97a9230107aa72b231f78952c0f178b71a920f036d360518480bdc'}, + {'cuda-samples-11.6_multiple-sms.patch': '8849e4882d797d155d6ebb71377fa1409205361776ade8da699452a4ecb94a0a'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '12.2.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " +local_filters += "Samples/6_Performance/LargeKernelParameter/Makefile " + +buildopts = "HOST_COMPILER=g++ SMS='%%(cuda_cc_space_sep_no_period)s' FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch new file mode 100644 index 00000000000..b6613f6a3c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.3_multiple-sms.patch @@ -0,0 +1,31 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile cuda-samples-11.3/Samples/memMapIPCDrv/Makefile +--- cuda-samples-11.3.orig/Samples/memMapIPCDrv/Makefile 2024-07-29 13:17:10.330743000 +0200 ++++ cuda-samples-11.3/Samples/memMapIPCDrv/Makefile 2024-07-29 13:19:13.158507504 +0200 +@@ -321,6 +321,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -401,7 +407,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch new file mode 100644 index 00000000000..8c4e36f7e74 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/cuda-samples-11.6_multiple-sms.patch @@ -0,0 +1,56 @@ +# Fixes "nvcc fatal: Option '--ptx (-ptx)' is not allowed when compiling for multiple GPU architectures" +# fatal compilation issue when building for multiple SM architectures +# More info, see https://github.com/NVIDIA/cuda-samples/issues/289 + +# Author: Caspar van Leeuwen + +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 12:14:28.538848000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/memMapIPCDrv/Makefile 2024-07-29 13:02:45.134261829 +0200 +@@ -313,6 +313,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -394,7 +400,7 @@ + endif + + $(PTX_FILE): memMapIpc_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) +diff -Nru cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile +--- cuda-samples-12.2.orig/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 12:14:28.546771000 +0200 ++++ cuda-samples-12.2/Samples/3_CUDA_Features/ptxjit/Makefile 2024-07-29 13:02:38.741961008 +0200 +@@ -307,6 +307,12 @@ + ifneq ($(HIGHEST_SM),) + GENCODE_FLAGS += -gencode arch=compute_$(HIGHEST_SM),code=compute_$(HIGHEST_SM) + endif ++ ++# Generate the explicit PTX file for the lowest SM architecture in $(SMS), so it works on all SMS listed there ++LOWEST_SM := $(firstword $(sort $(SMS))) ++ifneq ($(LOWEST_SM),) ++GENCODE_FLAGS_LOWEST_SM += -gencode arch=compute_$(LOWEST_SM),code=compute_$(LOWEST_SM) ++endif + endif + + ifeq ($(TARGET_OS),darwin) +@@ -390,7 +396,7 @@ + endif + + $(PTX_FILE): ptxjit_kernel.cu +- $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS) -o $@ -ptx $< ++ $(EXEC) $(NVCC) $(INCLUDES) $(ALL_CCFLAGS) $(GENCODE_FLAGS_LOWEST_SM) -o $@ -ptx $< + $(EXEC) mkdir -p data + $(EXEC) cp -f $@ ./data + $(EXEC) mkdir -p ../../../bin/$(TARGET_ARCH)/$(TARGET_OS)/$(BUILD_TYPE) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb new file mode 100644 index 00000000000..24c7b5f5c90 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.6.0.eb @@ -0,0 +1,22 @@ +name = 'CUDA' +version = '12.6.0' +local_nv_version = '560.28.03' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '31ab04394e69b14dd8656e2b44c2877db1a0e898dff8a7546a4c628438101b94', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '398db7baca17d51ad5035c606714c96380c965fd1742478c743bc6bbb1d8f63c' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..c1f83cad099 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CUDD' +version = '3.0.0' + +homepage = 'https://github.com/ivmai/cudd' +description = """The CUDD package is a package written in C for the manipulation of + decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision + diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce'] + +sanity_check_paths = { + 'files': ['include/cudd.h', 'lib/libcudd.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3322e6b4b56 --- /dev/null +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-3.4.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'CUTLASS' +version = '3.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cutlass' +description = """CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['49f4b854acc2a520126ceefe4f701cfe8c2b039045873e311b1f10a8ca5d5de1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), +] + +_copts = [ + '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"', + '-DCUTLASS_ENABLE_CUBLAS=1', + '-DCUTLASS_ENABLE_CUDNN=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..1bd10280160 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2022a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('petsc4py', '3.17.4'), + ('slepc4py', '3.17.2'), + ('scikit-learn', '1.1.2'), + ('scVelo', '0.2.5'), + ('scanpy', '1.9.1'), # also provides anndata + ('numba', '0.56.4'), + ('networkx', '2.8.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +_preinstallopts_pygam = """sed -i -e 's/numpy = .*/numpy = "^1.22.3"/g' """ +_preinstallopts_pygam += """-e 's/scipy = .*/scipy = "^1.8.1"/g' pyproject.toml && """ + +exts_list = [ + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('python-utils', '3.8.1', { + 'checksums': ['ec3a672465efb6c673845a43afcfafaa23d2594c24324a40ec18a0c59478dc0b'], + }), + ('progressbar2', '4.3.2', { + 'modulename': 'progressbar', + 'checksums': ['c37e6e1b4e57ab43f95c3d0e8d90061bec140e4fed56b8343183db3aa1e19a52'], + }), + ('pygam', '0.9.0', { + 'patches': ['pygam-0.9.0_fix-poetry.patch'], + 'checksums': [ + {'pygam-0.9.0.tar.gz': 'dba62285a275cdd15a6adf764f6717b3cd077502f01cf1bcee5ce7cbda221956'}, + {'pygam-0.9.0_fix-poetry.patch': '90460a5416167f146f5bf2c55e46c23d1e7a8f864652e24665354a1b39d7e3d0'}, + ], + 'preinstallopts': _preinstallopts_pygam, + }), + ('pygpcca', '1.0.4', { + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + 'preinstallopts': "sed -i 's/jinja2==/jinja2>=/g' requirements.txt && ", + }), + ('cellrank', version, { + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + # strip away too strict version requirements for pandas + anndata + 'preinstallopts': "sed -i -e 's/pandas>=1.5.0/pandas/g' -e 's/anndata>=0.9/anndata/g' pyproject.toml && ", + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import cellrank as cr'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3ec16f6ab04 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-2.0.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '2.0.2' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scVelo', '0.3.1'), + ('Seaborn', '0.13.2'), + ('wrapt', '1.15.0'), + ('PyTorch', '2.1.2', versionsuffix), + ('wandb', '0.16.1'), + ('PyTorch-Lightning', '2.2.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('nam', '0.0.3', { + 'checksums': ['48400d12b5f29fdd1671aebdf78d7f41bcac4f5c8ab7ed48770ee0c4fbc0673b'], + }), + ('python-utils', '3.8.2', { + 'checksums': ['c5d161e4ca58ce3f8c540f035e018850b261a41e7cb98f6ccf8e1deb7174a1f1'], + }), + ('progressbar2', '4.4.1', { + 'modulename': 'progressbar', + 'checksums': ['97d323ba03ad3d017a4d047fd0b2d3e733c5a360c07f87d269f96641c3de729f'], + }), + ('dunamai', '1.19.2', { + 'checksums': ['3be4049890763e19b8df1d52960dbea60b3e263eb0c96144a677ae0633734d2e'], + }), + ('poetry_dynamic_versioning', '1.2.0', { + 'checksums': ['1a7bbdba2530499e73dfc6ac0af19de29020ab4aaa3e507573877114e6b71ed6'], + }), + ('pygpcca', '1.0.4', { + 'preinstallopts': "sed -i 's/jinja2==3.0.3/jinja2>=3.0.3/' requirements.txt && ", + 'checksums': ['5e3b49279abc62d25133811daeee050715f995ff02042c46e2a2034331d090d1'], + }), + ('pygam', '0.9.1', { + 'checksums': ['a321a017bf485ed93fc6233e02621f8e7eab3d4f8971371c9ae9e079c55be01d'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + (name, version, { + 'modulename': 'cellrank', + 'preinstallopts': "sed -i 's/matplotlib>=3.5.0,<3.7.2/matplotlib>=3.5.0/' pyproject.toml && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['47c1d2e953ac91f572937d816142b4ac5f0c876174c60f857562de76a9f8aa61'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch new file mode 100644 index 00000000000..cc463d4ea64 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/pygam-0.9.0_fix-poetry.patch @@ -0,0 +1,26 @@ +workaround for: + RuntimeError: The Poetry configuration is invalid: + - Additional properties are not allowed ('group' was unexpected) +author: Kenneth Hoste (HPC-UGent) +--- pygam-0.9.0/pyproject.toml.orig 2024-01-05 22:13:47.399107878 +0100 ++++ pygam-0.9.0/pyproject.toml 2024-01-05 22:13:52.323119792 +0100 +@@ -12,19 +12,6 @@ + scipy = "^1.10.1" + progressbar2 = "^4.2.0" + +-[tool.poetry.group.dev.dependencies] +-pytest = "^7.2.2" +-flake8 = "^6.0.0" +-codecov = "^2.1.12" +-pytest-cov = "^4.0.0" +-mock = "^5.0.1" +-nbsphinx = "^0.9.0" +-sphinx-rtd-theme = "^1.2.0" +-sphinxcontrib-napoleon = "^0.7" +-ipython = "^8.11.0" +-pandas = "^1.5.3" +-black = "^23.1.0" +- + [tool.black] + line-length = 88 + skip-string-normalization = true diff --git a/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..947a6afdad5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-17.0.0_20230515-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '17.0.0_20230515' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'c5dede880d17' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ["https://github.com/llvm/llvm-project/archive"], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': 'llvm-project-%s.tar.gz' % version, +}] +checksums = ['6f371f9ac208b8e9dc57fc117b1a9c8565d7ea2bbb49a2768cb9c3c0fee0291d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8b096078c89 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-18.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '18.1.8' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['0b58557a6d32ceee97c8d533a59b9212d87e0fc4d2833924eb6c611247db2f2a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Perl', '5.38.2'), + # Including Python bindings would require this as a runtime dep + # and SWIG as an additional build dep + ('Python', '3.12.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.42'), + ('hwloc', '2.10.0'), + ('libxml2', '2.12.7'), + ('ncurses', '6.5'), + ('GMP', '6.3.0'), + ('Z3', '4.13.0'), +] + +# If True, Flang does not currently support building with LLVM exceptions enabled. +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b43a426454f --- /dev/null +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'ConcurrentVersionsSystem' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of +Source Configuration Management (SCM). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = ['cvs-%(version)s.tar.bz2'] +patches = [ + 'CVS-1.11.23-zlib-1.patch', + 'CVS-1.11.23-getline.patch', +] +checksums = [ + '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9', # cvs-1.11.23.tar.bz2 + # CVS-1.11.23-zlib-1.patch + '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4', + # CVS-1.11.23-getline.patch + '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874', +] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('zlib', '1.3.1') +] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..60e5009dc91 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.5" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +checksums = ['cd328edeac92f6a665de9f323c93b712af1858bc2e0d88f3f7100469470a1b8a'] + +builddependencies = [('binutils', '2.42')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6b2414be446 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e030f21ba6c --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.3.0.eb @@ -0,0 +1,52 @@ +# Copyright:: Copyright 2019-2024 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c9e419d570a --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.10' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2622f010126 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.18.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('pixman', '0.43.4'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('X11', '20240607'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5a6b4ee2256 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.10.2-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.10.2' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['108100960bb7e64573ea925af2ee7611701241abb36ce0aae3354528403a7d87'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('zstd', '1.5.6'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 9a0eeba1628..1556b0f9dad 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -45,12 +45,6 @@ preinstallopts = "sed -i 's/theano/Theano-PyMC/g' setup.py && " use_pip = True -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} - exts_list = [ ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb new file mode 100644 index 00000000000..b6b2b66159c --- /dev/null +++ b/easybuild/easyconfigs/c/cfgrib/cfgrib-0.9.14.0-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'cfgrib' +version = '0.9.14.0' + +homepage = 'https://github.com/ecmwf/cfgrib/' +description = """ +A Python interface to map GRIB files to the NetCDF Common Data Model following the CF +Convention using ecCodes. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ecCodes', '2.31.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('findlibs', '0.0.5', { + 'checksums': ['7a801571e999d0ee83f9b92cbb598c21f861ee26ca9dba74cea8958ba4335e7e'], + }), + ('eccodes', '1.7.1', { + 'checksums': ['d3c7e9bab779d35b624cfd7b3331de111602cba6a6f6368efcc12407f30b2697'], + }), + (name, version, { + 'checksums': ['2b9a1e6bd47397e585f878ffd8aaac5969f6c9a448da767c700917b89c275bb2'], + }), +] + +sanity_check_commands = ['python -m cfgrib selfcheck'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb new file mode 100644 index 00000000000..b9964db690a --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-3.3.9-foss-2022b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '3.3.9' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """chewBBACA is a software suite for the creation and evaluation of core genome and whole genome +MultiLocus Sequence Typing (cg/wgMLST) schemas and results. The "BBACA" stands for "BSR-Based Allele Calling Algorithm". +BSR stands for BLAST Score Ratio as proposed by Rasko DA et al. The "chew" part adds extra coolness to the name and +could be thought of as "Comprehensive and Highly Efficient Workflow".""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + # Cython 3 is required, see https://github.com/althonos/pyrodigal/issues/40 + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('Cython', '3.0.8'), + ('Biopython', '1.81'), + ('plotly.py', '5.13.1'), + ('BLAST+', '2.14.0'), + ('prodigal', '2.6.3'), + ('MAFFT', '7.505', '-with-extensions'), + ('FastTree', '2.1.11'), + ('archspec', '0.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyrodigal', '3.5.1', { + 'checksums': ['20af59a6d968c88910b99d5f647bb7dd22d49e440ead95fe715cdd2c49f36e9f'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '7.0.0', { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), + ('SPARQLWrapper', '2.0.0', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + # relax numpy version requirement + 'preinstallopts': "sed -i 's/numpy~=1.24.3/numpy~=1.24.2/g' pyproject.toml && ", + 'runtest': "python setup.py test", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4bf0792b8cdd1783b50340ac713748ef2a351209cacb50ad4c9e2fe2e7fba772'], + }), +] + +sanity_check_paths = { + 'files': ['bin/chewBBACA.py', 'bin/chewie'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', + 'chewie --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b1788fb34f9 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,315 @@ +easyblock = 'Cargo' + +name = 'chopper' +version = '0.9.0' + +homepage = 'https://github.com/wdecoster/chopper' +description = """Rust implementation of NanoFilt+NanoLyse, both +originally written in Python. This tool, intended for long read +sequencing such as PacBio or ONT, filters and trims a fastq file. +Filtering is done on average read quality and minimal or maximal read +length, and applying a headcrop (start of read) and tailcrop (end of +read) while printing the reads passing the filter.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'wdecoster' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'chopper-0.9.0_fix_incorrect_version.patch', +] +checksums = [ + {'v0.9.0.tar.gz': 'ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'}, + {'anstyle-1.0.6.tar.gz': 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('libz-ng-sys', '1.1.15'), + ('libz-sys', '1.1.16'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.2'), + ('minimap2', '0.1.17+minimap2.2.27'), + ('minimap2-sys', '0.1.18+minimap2.2.27'), + ('miniz_oxide', '0.7.2'), + ('multimap', '0.9.1'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('ordered-float', '3.9.2'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pkg-config', '0.3.30'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.81'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rawpointer', '0.2.1'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.4'), + ('regex-automata', '0.4.6'), + ('regex-syntax', '0.8.3'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.15'), + ('ryu', '1.0.17'), + ('safe_arch', '0.7.1'), + ('semver', '0.1.20'), + ('serde', '1.0.198'), + ('serde_derive', '1.0.198'), + ('simba', '0.6.0'), + ('simdutf8', '0.1.4'), + ('statrs', '0.16.0'), + ('strsim', '0.11.1'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.60'), + ('thiserror', '1.0.58'), + ('thiserror-impl', '1.0.58'), + ('triple_accel', '0.4.0'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('vec_map', '0.8.2'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.16'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.5'), + ('windows_aarch64_gnullvm', '0.52.5'), + ('windows_aarch64_msvc', '0.52.5'), + ('windows_i686_gnu', '0.52.5'), + ('windows_i686_gnullvm', '0.52.5'), + ('windows_i686_msvc', '0.52.5'), + ('windows_x86_64_gnu', '0.52.5'), + ('windows_x86_64_gnullvm', '0.52.5'), + ('windows_x86_64_msvc', '0.52.5'), + ('xz2', '0.1.7'), +] +sanity_check_paths = { + 'files': ['bin/chopper'], + 'dirs': [], +} + +sanity_check_commands = [ + 'chopper --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch new file mode 100644 index 00000000000..57c15b94db4 --- /dev/null +++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch @@ -0,0 +1,28 @@ +Fix incorrect version number in the 0.9.0 tar file. + +Åke Sandgren, 2024-09-16 +diff --git a/Cargo.lock b/Cargo.lock +index 3e8f1fe..53fa5da 100644 +--- a/Cargo.lock ++++ b/Cargo.lock +@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" + + [[package]] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + dependencies = [ + "approx", + "atty", +diff --git a/Cargo.toml b/Cargo.toml +index f268dce..7f7277a 100644 +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -1,6 +1,6 @@ + [package] + name = "chopper" +-version = "0.8.0" ++version = "0.9.0" + authors = ["wdecoster "] + edition = "2021" + diff --git a/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..35921013c3e --- /dev/null +++ b/easybuild/easyconfigs/c/colorize/colorize-0.7.7-GCC-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RubyGem' + +name = 'colorize' +version = '0.7.7' + +homepage = 'https://github.com/fazibear/colorize' +description = """Ruby gem for colorizing text using ANSI escape sequences. +Extends String class or add a ColorizedString with methods to set the text color, background color and text effects.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['d6ab95a5fcdea3c36c3327d38c1e79e2950ee1788506d8489ae35db330937a99'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..247bb5ac24d --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'coxeter' +version = '20180226' +local_commit = '7b5a1f0' + +homepage = 'https://github.com/tscrim/coxeter' +description = """A library for the study of combinatorial aspects of Coxeter group theory""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/tscrim/coxeter/archive/%s/' % local_commit] +sources = [SOURCE_TAR_GZ] +patches = [ + 'coxeter-20180226_makefile.patch', + ('coxeter-20180226_sage_interface.patch', 0), +] +checksums = [ + {'coxeter-20180226.tar.gz': '5e0668c40b29c03c438a6ebc0f49f13aaf155b4bcbff56303a753390e6fce3aa'}, + {'coxeter-20180226_makefile.patch': '229ed201e41bae0ae7b22aa21d5007127aeb52fd158543dd5fff2e89797e211f'}, + {'coxeter-20180226_sage_interface.patch': '18ba75e51a944ffccb7fa440b823f68a0aad9066e8edcdd2b52bac6b43404bd3'}, +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' +preinstallopts = 'mkdir -p "%(installdir)s/bin" "%(installdir)s/lib" && ' +installopts = 'SAGE_LOCAL="%(installdir)s"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'lib/lib%%(name)s3.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'include/%(name)s', + 'share/%(name)s', + ] +} + +sanity_check_commands = ['echo "qq" | coxeter'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch new file mode 100644 index 00000000000..d00d6860689 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_makefile.patch @@ -0,0 +1,101 @@ +Allows installation of files needed for Sagemath +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/main/coxeter-makefile.patch +diff -u makefile.orig makefile +--- makefile.orig 2018-02-26 13:57:36.000000000 +0100 ++++ makefile 2024-08-16 14:15:51.889503570 +0200 +@@ -12,6 +12,7 @@ + gflags = -c $(includedirs) -g + + cflags = $(gflags) # the default setting ++cflags = -c $(includedirs) $(CPPFLAGS) $(CXXFLAGS) -fPIC + + ifdef optimize + NDEBUG = true +@@ -22,18 +23,74 @@ + cflags = $(pflags) + endif + +-cc = g++ ++EXENAME = coxeter ++LIBNAME = coxeter3 ++ifeq ($(UNAME),Darwin) ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .dylib ++ LIBDIR = lib ++ LINKFLAGS = -dynamiclib -Wl,-headerpad_max_install_names,-undefined,dynamic_lookup,-compatibility_version,3.0,-current_version,3.0,-install_name,$(SAGE_LOCAL)/lib/$(LIBPREFIX)$(LIBNAME)$(LIBEXT) ++ LINKLIBS = ++else ++ifeq ($(UNAME),CYGWIN) ++ EXEEXT = .exe ++ LIBPREFIX = cyg ++ LIBEXT = .dll ++ LIBDIR = bin ++ IMPLIB = lib$(LIBNAME).dll.a ++ LINKFLAGS = -shared -Wl,--out-implib=$(IMPLIB) -Wl,--export-all-symbols ++ LINKLIBS = -lc ++else ++ EXEEXT = ++ LIBPREFIX = lib ++ LIBEXT = .so ++ LIBDIR = lib ++ LINKFLAGS = $(LDFLAGS) -shared -Wl,-soname,libcoxeter3.so ++ LINKLIBS = -lc ++endif ++endif ++LIBRARY = $(LIBPREFIX)$(LIBNAME)$(LIBEXT) + +-all: coxeter #clean ++all: coxeter executable + + coxeter: $(objects) +- $(cc) -o coxeter $(objects) ++ $(CXX) $(LINKFLAGS) -o $(LIBRARY) $(objects) $(LINKLIBS) ++ ++executable: $(objects) ++ $(CXX) $(LDFLAGS) -o $(EXENAME)$(EXEEXT) $(objects) ++ ++DATADIR="$$SAGE_LOCAL/share/coxeter/" ++INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/" ++LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)" ++ ++install: coxeter executable ++ cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/" ++ cp $(LIBRARY) $(LIBRARYDIR) ++ if [ $(UNAME) = "CYGWIN" ]; then \ ++ cp $(IMPLIB) "$$SAGE_LOCAL/lib/"; \ ++ fi ++ ++ mkdir -p $(DATADIR) ++ cp -r coxeter_matrices headers messages $(DATADIR) ++ mkdir -p $(INCLUDEDIR) ++ cp -r *.h *.hpp $(INCLUDEDIR) ++ ++check: coxeter executable ++ $(EXENAME)$(EXEEXT) < test.input > test.output ++ ++ if ! diff test.output.expected test.output > /dev/null; then \ ++ echo >&2 "Error testing coxeter on test.input:"; \ ++ diff test.output.expected test.output; \ ++ exit 1; \ ++ fi ++ rm -f test.output + + clean: + rm -f $(objects) + + %.o:%.cpp +- $(cc) $(cflags) $*.cpp ++ $(CXX) $(cflags) $*.cpp + + # dependencies --- these were generated automatically by make depend on my + # system; they are explicitly copied for portability. Only local dependencies +@@ -43,7 +100,7 @@ + # contents of tmp in lieu of the dependencies listed here. + + %.d:%.cpp +- @$(cc) -MM $*.cpp ++ @$(CXX) -MM $*.cpp + depend: $(dependencies) + + affine.o: affine.cpp affine.h globals.h coxgroup.h coxtypes.h io.h list.h \ diff --git a/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch new file mode 100644 index 00000000000..2b4cd427ca9 --- /dev/null +++ b/easybuild/easyconfigs/c/coxeter/coxeter-20180226_sage_interface.patch @@ -0,0 +1,89 @@ +Adds sage interface. See https://github.com/tscrim/coxeter/pull/14 +Source: https://gitlab.archlinux.org/archlinux/packaging/packages/coxeter/-/blob/git.20180226-4/coxeter-sage.patch +diff -u /dev/null sage.h +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.h 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,23 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#ifndef SAGE_H /* guard against multiple inclusions */ ++#define SAGE_H ++ ++#include "globals.h" ++#include "coxgroup.h" ++#include "coxtypes.h" ++#include "schubert.h" ++#include "list.h" ++ ++namespace sage { ++ using namespace coxeter; ++ using namespace coxtypes; ++ using namespace list; ++ ++ void interval(List& result, CoxGroup& W, const CoxWord& g, const CoxWord& h); ++} ++ ++#endif +diff -u /dev/null sage.cpp +--- /dev/null 2024-08-27 08:29:37.672016778 +0200 ++++ sage.cpp 2024-08-27 12:17:23.716096310 +0200 +@@ -0,0 +1,56 @@ ++/* ++ Coxeter version 3.0 Copyright (C) 2009 Mike Hansen ++ See file main.cpp for full copyright notice ++*/ ++ ++#include "sage.h" ++ ++namespace sage { ++ ++ void interval(List& list, CoxGroup& W, const CoxWord& g, const CoxWord& h) ++ ++ /* ++ Returns a list of the elements in the Bruhat interval between g and h. ++ Note that this assumes that g and h are in order. ++ */ ++ { ++ if (not W.inOrder(g,h)) { ++ return; ++ } ++ ++ W.extendContext(h); ++ ++ CoxNbr x = W.contextNumber(g); ++ CoxNbr y = W.contextNumber(h); ++ ++ BitMap b(W.contextSize()); ++ W.extractClosure(b,y); ++ ++ BitMap::ReverseIterator b_rend = b.rend(); ++ List res(0); ++ ++ for (BitMap::ReverseIterator i = b.rbegin(); i != b_rend; ++i) ++ if (not W.inOrder(x,*i)) { ++ BitMap bi(W.contextSize()); ++ W.extractClosure(bi,*i); ++ CoxNbr z = *i; // andnot will invalidate iterator ++ b.andnot(bi); ++ b.setBit(z); // otherwise the decrement will not be correct ++ } else ++ res.append(*i); ++ ++ schubert::NFCompare nfc(W.schubert(),W.ordering()); ++ Permutation a(res.size()); ++ sortI(res,nfc,a); ++ ++ list.setSize(0); ++ for (size_t j = 0; j < res.size(); ++j) { ++ CoxWord w(0); ++ W.schubert().append(w, res[a[j]]); ++ list.append(w); ++ } ++ ++ return; ++ } ++ ++} diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3043857d925 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..49c61ff64fb --- /dev/null +++ b/easybuild/easyconfigs/c/cramino/cramino-0.14.5-GCC-12.3.0.eb @@ -0,0 +1,351 @@ +easyblock = 'Cargo' + +name = 'cramino' +version = '0.14.5' + +homepage = 'https://github.com/wdecoster/cramino' +description = """A tool for quick quality assessment of cram and bam files, intended for long read sequencing.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/cramino/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.14.5.tar.gz': 'd3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032'}, + {'ahash-0.8.9.tar.gz': 'd713b3834d76b85304d4d525563c1276e2e30dc97cc67bfb4585a4a29fc2c89f'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'}, + {'anstream-0.6.12.tar.gz': 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('derive-new', '0.5.9'), + ('either', '1.10.0'), + ('env_filter', '0.1.0'), + ('env_logger', '0.11.2'), + ('equivalent', '1.0.1'), + ('flatbuffers', '23.5.26'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.2.12'), + ('glob', '0.3.1'), + ('half', '2.3.1'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hts-sys', '2.1.1'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '2.2.3'), + ('itertools', '0.12.1'), + ('itoa', '1.0.10'), + ('js-sys', '0.3.68'), + ('lazy_static', '1.4.0'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.153'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.15'), + ('linear-map', '1.2.0'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.1'), + ('newtype_derive', '0.1.6'), + ('num', '0.4.1'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-iter', '0.1.44'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.18'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.2.3+3.2.1'), + ('openssl-sys', '0.9.100'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('proc-macro2', '1.0.78'), + ('quick-error', '1.2.3'), + ('quote', '1.0.35'), + ('rayon', '1.8.1'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.5'), + ('regex-syntax', '0.8.2'), + ('rust-htslib', '0.46.0'), + ('rustc_version', '0.1.7'), + ('rustc_version', '0.4.0'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.17'), + ('semver', '0.1.20'), + ('semver', '1.0.22'), + ('serde', '1.0.197'), + ('serde_derive', '1.0.197'), + ('serde_json', '1.0.114'), + ('static_assertions', '1.1.0'), + ('strsim', '0.11.0'), + ('strum_macros', '0.25.3'), + ('syn', '1.0.109'), + ('syn', '2.0.50'), + ('thiserror', '1.0.57'), + ('thiserror-impl', '1.0.57'), + ('tiny-keccak', '2.0.2'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.0'), + ('utf8parse', '0.2.1'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.91'), + ('wasm-bindgen-backend', '0.2.91'), + ('wasm-bindgen-macro', '0.2.91'), + ('wasm-bindgen-macro-support', '0.2.91'), + ('wasm-bindgen-shared', '0.2.91'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.52.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb new file mode 100644 index 00000000000..c9e4de852a5 --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-GCC-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Ruby', '3.3.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('bio', '1.6.0.pre.20181210', { + 'checksums': ['c4114aeb99b012f90660b92ead4ca88c1578fd58252ed3ec46eb45dc4a2c6cc9'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1f54c552c2e --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.9-GCCcore-12.3.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.9' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Cython', '3.0.8'), # required for dnaio +] + +dependencies = [ + ('pigz', '2.8'), + ('Python', '3.11.3'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # note: newer xopen versions require newer python-isal + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '1.2.1', { + 'checksums': ['4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38'], + }), + (name, version, { + 'checksums': ['da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64022827805 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('OpenSSL', '3', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7120c9c13e --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ca182becfcd --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DBus' +version = '1.15.8' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('expat', '2.6.2'), +] + +configopts = '-DENABLE_SYSTEMD=OFF ' +# disable documentation +configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index c1457cc041c..24a8b13835c 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -33,6 +33,7 @@ builddependencies = [ ] dependencies = [ + ('Perl', '5.36.1'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), ('BamTools', '2.5.2'), @@ -45,16 +46,20 @@ buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make runtest = 'test' -files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] +files_to_copy = [ + (['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*', '../rsem-eval/*.pm'], 'bin'), +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', - 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', - 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-parse-alignments', 'rsem_perl_utils.pm', 'rsem-plot-model', 'rsem-preref', + 'rsem-sam-validator', 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', 'rsem-synthesis-reference-transcripts']], 'dirs': [], } +sanity_check_commands = [r"rsem-eval-calculate-score --help 2>&1 | grep 'rsem-eval-calculate-score \[options\]'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb new file mode 100644 index 00000000000..c862fcea552 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -0,0 +1,93 @@ +easyblock = 'CMakeMake' + +name = 'DFTB+' +version = '24.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +_external_extract = 'mkdir -p %s && tar -C %s' % (_external_dir, _external_dir) +_external_extract += ' --strip-components=1 -xzf %%s' + +source_urls = ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'] +sources = [ + 'dftbplus-%(version)s.tar.xz', + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'fbe3d62127d86bd8e49ad25a1e5793e6a095e8e7.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('slakos', 'slakos'), + }, + { + # GBSA (gbsa) data for testing + 'source_urls': ['https://github.com/grimme-lab/gbsa-parameters/archive'], + 'download_filename': '6836c4d997e4135e418cfbe273c96b1a3adb13e2.tar.gz', + 'filename': 'gbsa-data-%(version)s.tar.gz', + 'extract_cmd': _external_extract % ('gbsa', 'gbsa'), + }, +] +checksums = [ + {'dftbplus-24.1.tar.xz': '3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'}, + {'slakos-data-24.1.tar.gz': '78a0494c2ff9216d6a9199ba07d632b18b809e0198f43905c044b5748bde488d'}, + {'gbsa-data-24.1.tar.gz': 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('dftd4', '3.7.0'), + ('ELSI', '2.11.0', '-PEXSI'), + ('libmbd', '0.12.6'), +] + +# Prefer dependencies from EB than bundled sources +configopts = '-DHYBRID_CONFIG_METHODS="Find;Submodule;Fetch" ' +configopts += '-DWITH_MPI=1 -DWITH_OMP=1 -DWITH_SDFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DBUILD_SHARED_LIBS=1 -DWITH_API=1 -DWITH_PYTHON=0 ' # Python bindings installed as extension +configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' + +runtest = 'test' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'runtest': False, +} +exts_list = [ + ('dptools', version, { + 'source_tmpl': 'dftbplus-%(version)s.tar.xz', + 'source_urls': ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'], + 'start_dir': 'tools/dptools', + 'checksums': ['3bc405d1ab834b6b145ca671fb44565ec50a6f576e9e18e7a1ae2c613a311321'], + }), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']] + + ['lib/libdftbplus.%s' % SHLIB_EXT, 'lib/libmpifx.%s' % SHLIB_EXT], + 'dirs': ['include/dftbplus', 'lib/cmake', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import dptools'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..379eb0439bb --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2', versionsuffix), + ('ESM-2', '2.0.0', versionsuffix), # for fair-esm + ('PyTorch', '2.1.2', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb new file mode 100644 index 00000000000..558d3f61871 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('ONNX-Runtime', '1.19.2'), + ('ESM-2', '2.0.0'), # for fair-esm + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', '2.2.1'), + ('Transformers', '4.39.3'), + ('SentencePiece', '0.2.0'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.7.1', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['851545804b08413a3f27fd5131edefc30acfdee513919eebabb29678d8632218'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb new file mode 100644 index 00000000000..db41d0c240f --- /dev/null +++ b/easybuild/easyconfigs/d/dblatex/dblatex-0.3.12-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'dblatex' +version = '0.3.12' + +homepage = 'https://dblatex.sourceforge.net/' +description = """dblatex is a program that transforms your SGML/XML DocBook documents to DVI, + PostScript or PDF by translating them into pure LaTeX as a first process. + MathML 2.0 markups are supported, too. It started as a clone of DB2LaTeX.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://master.dl.sourceforge.net/project/dblatex/dblatex/dblatex-%(version)s/'] +sources = ['%(name)s3-%(version)s.tar.bz2'] +checksums = ['16e82786272ed1806a079d37914d7ba7a594db792dc4cc34c1c3737dbd4da079'] + +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), + ('texlive', '20230313'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'dbtexmf.dblatex'} + +postinstallcmds = ["cp -r %(builddir)s/%(name)s3-%(version)s/scripts %(installdir)s/bin"] + +sanity_check_commands = ['dblatex --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb new file mode 100644 index 00000000000..3e1eb388a12 --- /dev/null +++ b/easybuild/easyconfigs/d/decona/decona-1.4-20240731-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'decona' +version = '1.4-20240731' +local_commit = 'f7488ad' + +homepage = 'https://github.com/Saskia-Oosterbroek/decona' +description = "fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Saskia-Oosterbroek/decona/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['7504160481ccdd3410fc79348c01a9a3bf0795ad73679cc305e1dcdf3e395962'] + +dependencies = [ + ('Python', '3.11.3'), + ('NanoFilt', '2.8.0'), + ('qcat', '1.1.0'), + ('CD-HIT', '4.8.1'), + ('minimap2', '2.26'), + ('Racon', '1.5.0'), + ('medaka', '1.11.3'), + ('BLAST+', '2.14.1'), +] + +fix_python_shebang_for = ['decona'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['decona'], + 'dirs': [], +} + +sanity_check_commands = ["decona -v | grep 'This is Decona %s'" % version.split('-')[0]] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb new file mode 100644 index 00000000000..912ed2baf4a --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.7.0-foss-2023a.eb @@ -0,0 +1,50 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) +# C. Willemyns (Vrije Universiteit Brussel) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.7.0' + +homepage = 'https://dftd4.readthedocs.io' +description = """ +The dftd4 project provides an implementation of the generally applicable, charge dependent +London-dispersion correction, termed DFT-D4. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), + ('multicharge', '0.3.0'), +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.h'], + 'dirs': ['include/dftd4', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..f04774b1b55 --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0', versionsuffix), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0b97a82cfde --- /dev/null +++ b/easybuild/easyconfigs/d/dictys/dictys-1.1.0-foss-2023a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'dictys' +version = '1.1.0' + +homepage = 'https://github.com/pinellolab/dictys' +description = "Context specific and dynamic gene regulatory network reconstruction and analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('pybedtools', '0.9.1'), + ('SAMtools', '1.18'), + ('MACS2', '2.2.9.1'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('h5py', '3.9.0'), + ('pyro-ppl', '1.9.0'), + ('adjustText', '0.7.3'), + ('Pysam', '0.22.0'), + ('paramiko', '3.2.0'), + ('Jupyter-bundle', '20230823'), + ('Qtconsole', '5.5.1'), + ('junos-eznc', '2.7.1'), +] + +# regenerate WellingtonC.c to works with python 3.11 + unpin matplotlib version +local_pyDNase_preinstallopts = ( + "cd pyDNase/footprinting && rm WellingtonC.c && cythonize -i WellingtonC.pyx && cd .. && cd .. && " + "sed -i 's/matplotlib < 2.0.0/matplotlib/' setup.py && " +) + +exts_list = [ + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('pynetbox', '7.4.0', { + 'checksums': ['fd0b1f197b3880048408ff5ed84422dd599bcd9389e32cb06a09b9b0d55c1636'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('aerleon', '1.9.0', { + 'checksums': ['850cd621dda750263db313d4473302b48b82adaaa9220e6fd0677cb7900f95f6'], + }), + ('homer', '0.7.0', { + 'checksums': ['efaf9b3948f6aecdf88cc87c0296a18aed77c152489a7f85c571965fb16f9e57'], + }), + ('pyDNase', '0.3.0', { + 'preinstallopts': local_pyDNase_preinstallopts, + 'modulename': 'pyDNase', + 'checksums': ['dba03cadca37929a1cc41545e962136f29efc41f8e3c6de042c51c47ee04d558'], + }), + (name, version, { + 'checksums': ['59610a8c57e9fc525ec5d13b69efc8b513c78a85a595e0e2b0138da62a035978'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["dictys --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c3ffb7be647 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'dlib' +version = '19.24.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +# dlib can use BLAS/LAPACK, so using full toolchain +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +patches = ['dlib-19.24.6_FlexiBLAS.patch'] +checksums = [ + {'dlib-19.24.6.tar.gz': '77e3c28ac2c66141514b07cbb74b7c7f80381c019ce5fec99007980bc6490d7d'}, + {'dlib-19.24.6_FlexiBLAS.patch': '47fb348d5f1cd064a135d33cf49fdef56ade24a64218311743076cb6b313738b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('Python', '3.11.3'), + ('libjxl', '0.8.2'), + ('X11', '20230603'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " +preinstallopts += "sed -i 's/BLAS_REFERENCE cblas/BLAS_REFERENCE flexiblas/g' dlib/cmake_utils/find_blas.cmake && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch new file mode 100644 index 00000000000..bb12f35adbc --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.24.6_FlexiBLAS.patch @@ -0,0 +1,25 @@ +use FlexiBLAS as BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) +diff -ru dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake dlib-19.24.6/dlib/cmake_utils/find_blas.cmake +--- dlib-19.24.6.orig/dlib/cmake_utils/find_blas.cmake 2024-02-18 14:43:31.000000000 +0100 ++++ dlib-19.24.6/dlib/cmake_utils/find_blas.cmake 2024-09-20 20:35:35.927348475 +0200 +@@ -66,17 +66,15 @@ + + # First, search for libraries via pkg-config, which is the cleanest path + find_package(PkgConfig) +- pkg_check_modules(BLAS_REFERENCE cblas) +- pkg_check_modules(LAPACK_REFERENCE lapack) ++ pkg_check_modules(BLAS_REFERENCE flexiblas) + # Make sure the cblas found by pkgconfig actually has cblas symbols. + SET(CMAKE_REQUIRED_LIBRARIES "${BLAS_REFERENCE_LDFLAGS}") + CHECK_FUNCTION_EXISTS(cblas_ddot PKGCFG_HAVE_CBLAS) + if (BLAS_REFERENCE_FOUND AND LAPACK_REFERENCE_FOUND AND PKGCFG_HAVE_CBLAS) + set(blas_libraries "${BLAS_REFERENCE_LDFLAGS}") +- set(lapack_libraries "${LAPACK_REFERENCE_LDFLAGS}") + set(blas_found 1) + set(lapack_found 1) +- set(REQUIRES_LIBS "${REQUIRES_LIBS} cblas lapack") ++ set(REQUIRES_LIBS "${REQUIRES_LIBS} flexiblas") + message(STATUS "Found BLAS and LAPACK via pkg-config") + return() + endif() diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..e292bfcc18b --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,80 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.6.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['dorado-0.6.1_include-fstream.patch'] +checksums = [ + None, + 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch new file mode 100644 index 00000000000..c1165f3fe5c --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..0e32e9616ca --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,89 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.7.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = [ + '%(name)s-%(version)s_include-fstream.patch', + '%(name)s-%(version)s_dont_install_external_libraries.patch', +] + +checksums = [ + None, + 'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530', + '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), + ('HTSlib', '1.18'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# disable treating warnings like errors by stripping out -Werror +# cfr. https://github.com/nanoporetech/dorado/issues/779 +preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " + +_copts = [ + "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", + "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", + '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', + "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib", + # add -pthread flag (in addition to -lpthread) to avoid linking error: + # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' + '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', +] + +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch new file mode 100644 index 00000000000..67bd9efee78 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_dont_install_external_libraries.patch @@ -0,0 +1,54 @@ +Don't install external libraries in Dorado's lib directory. + +Åke Sandgren, 2024-09-02 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index a84c7524..0791dda8 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -431,7 +431,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + else() + # bundle the libraries from the cuda toolkit + file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}") +- install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs) + endif() + endforeach() + +@@ -444,14 +444,14 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + RESOLVE_SYMLINKS("${DEBUG_LIBRARIES}" NEW_HDF_DEBUG_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_DEBUG_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Debug) + endif() + endforeach() + FILTER_LIST("${HDF5_C_LIBRARIES}" RELEASE_LIBRARIES optimized debug ${SHARED_LIB_EXT}) + RESOLVE_SYMLINKS("${RELEASE_LIBRARIES}" NEW_HDF_RELEASE_LIBRARIES) + foreach(HDF_LIB IN LISTS NEW_HDF_RELEASE_LIBRARIES) + if(${HDF_LIB} MATCHES "hdf5") +- install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) ++ #install(FILES ${HDF_LIB} DESTINATION lib COMPONENT redist_libs CONFIGURATIONS Release ReleaseWithDebInfo) + endif() + endforeach() + endif() +@@ -459,17 +459,17 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux") + find_library(SZ_DLL sz REQUIRED) + get_filename_component(SZ_DLL_PATH ${SZ_DLL} DIRECTORY) + file(GLOB SZ_DLLS "${SZ_DLL_PATH}/libsz.so*") +- install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${SZ_DLLS} DESTINATION lib COMPONENT redist_libs) + + find_library(AEC_DLL aec REQUIRED) + get_filename_component(AEC_DLL_PATH ${AEC_DLL} DIRECTORY) + file(GLOB AEC_DLLS "${AEC_DLL_PATH}/libaec.so*") +- install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${AEC_DLLS} DESTINATION lib COMPONENT redist_libs) + + # If zstd has been dynamically linked, add the .so to the package + get_filename_component(ZSTD_LIBRARY_PATH ${ZSTD_LIBRARY_RELEASE} DIRECTORY) + file(GLOB ZSTD_DLLS "${ZSTD_LIBRARY_PATH}/*zstd.so*") +- install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) ++ #install(FILES ${ZSTD_DLLS} DESTINATION lib COMPONENT redist_libs) + + elseif(WIN32) + file(GLOB TORCH_DLLS "${TORCH_LIB}/lib/*.dll") diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch new file mode 100644 index 00000000000..bf8d2346e5d --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.7.3_include-fstream.patch @@ -0,0 +1,27 @@ +add missing include to fix compiler errors like: + + error: variable std::ofstream summary_out has initializer but incomplete type + +see also https://github.com/nanoporetech/dorado/pull/780 + +author: Kenneth Hoste (HPC-UGent) +--- dorado/dorado/cli/duplex.cpp.orig 2024-04-30 17:59:15.483935823 +0200 ++++ dorado/dorado/cli/duplex.cpp 2024-04-30 17:59:34.658694274 +0200 +@@ -39,6 +39,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- dorado/dorado/cli/demux.cpp.orig 2024-04-30 18:13:40.327122548 +0200 ++++ dorado/dorado/cli/demux.cpp 2024-04-30 18:15:37.576760942 +0200 +@@ -17,6 +17,7 @@ + #include + + #include ++#include + #include + #include + #include \ No newline at end of file diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb new file mode 100644 index 00000000000..5143b629849 --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.5-gompi-2024a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.5' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c3d672fcf1be81e9afb65ef3f860a7dfe0f1bd79360ac63848acfe4d44439c9'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('lwgrp', '1.0.6'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cfd077260fb --- /dev/null +++ b/easybuild/easyconfigs/d/dub/dub-1.38.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'dub' +version = '1.38.1' + +homepage = 'https://github.com/dlang/dub' +description = "Package and build manager for D applications and libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/dlang/dub/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a7c9a2f819fdea7359f298cba76e81a24ca1536d756c3b4b98c2480463c37907'] + +builddependencies = [ + ('binutils', '2.40'), + ('LDC', '1.39.0'), +] + +cmds_map = [('.*', "ldmd2 -v -run build.d")] + +files_to_copy = [(['bin/dub'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/dub'], + 'dirs': [], +} + +sanity_check_commands = ["dub --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb new file mode 100644 index 00000000000..fb67d050e02 --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2023a.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +_minimap2_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.4'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('h5py', '3.9.0'), + ('pod5-file-format', '0.3.10'), + ('parasail', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap2_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyfastx', '2.0.1', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55'], + }), + (name, version, { + 'sources': [{'download_filename': 'duplex_tools-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pyfastx --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb new file mode 100644 index 00000000000..a1be84f6de9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0-foss-2023a-PEXSI.eb @@ -0,0 +1,47 @@ +name = 'ELSI' +version = '2.11.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://gitlab.com/elsi_project/elsi_interface/-/archive/v2.11.0/'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'ELSI-2.11.0_bison_3.8_compat.patch', +] +checksums = [ + {'elsi_interface-v2.11.0.tar.gz': '2e6929827ed9c99a32381ed9da40482e862c28608d59d4f27db7dcbcaed1520d'}, + {'ELSI-2.11.0_bison_3.8_compat.patch': 'a1284f5c0f442129610aa0fb463cc2b54450e3511a2fd6c871fadc21a16e9504'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('ELPA', '2023.05.001'), + ('NTPoly', '3.1.0'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +# Tests use 4 MPI ranks, they require a minimum of 4 cores +# Map each MPI process to a single CPU core to avoid tests fails +pretestopts = "export OMPI_MCA_rmaps_base_mapping_policy=slot:PE=1 && " + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch new file mode 100644 index 00000000000..255ed4a5575 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.11.0_bison_3.8_compat.patch @@ -0,0 +1,14 @@ +Make it compatible with Bison 3.7 +Author: Åke Sandgren, 20211020 +Update: Cintia Willemyns (Vrije Universiteit Brussel) +--- elsi_interface-v2.11.0.orig/external/SCOTCH/CMakeLists.txt 2024-09-10 19:01:11.447551000 +0200 ++++ elsi_interface-v2.11.0/external/SCOTCH/CMakeLists.txt 2024-09-10 19:08:44.913993743 +0200 +@@ -56,7 +56,7 @@ + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c + # Versions of bison > 2.X insert a '#include tmp2.h' in tmp2.c. A simple 'mv' will not work. + # The file needs to remain in the directory with the old name. Hence the 'cp' +- COMMAND cp ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h ++ COMMAND ln -s ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h + COMMAND flex -Pscotchyy -o${PROJECT_BINARY_DIR}/generated/tmp1.c ${SCOTCH_DIR}/parser_ll.l + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp1.c ${PROJECT_BINARY_DIR}/generated/parser_ll.c + DEPENDS ${SCOTCH_DIR}/parser_yy.y ${SCOTCH_DIR}/parser_ll.l ${SCOTCH_DIR}/parser_yy.h ${SCOTCH_DIR}/parser_ll.h diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb new file mode 100644 index 00000000000..d5ef7e3da14 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.9.1-foss-2022a-PEXSI.eb @@ -0,0 +1,45 @@ +name = 'ELSI' +version = '2.9.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['https://wordpress.elsi-interchange.org/wp-content/uploads/2022/05'] +sources = ['elsi_interface-v%(version)s.tar.gz'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + {'elsi_interface-v2.9.1.tar.gz': 'ad3dc163159a79f7a83f360265f2446920c151ecce9c294136e630fe424f1d29'}, + {'pexsi-1.2.0-mpi30.patch': 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb'}, + {'ELSI-2.7.1_bison_3.7_compat.patch': '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('NTPoly', '2.7.1'), +] + +abs_path_compilers = True +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb new file mode 100644 index 00000000000..c68628823fb --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'EMMAX' +# version is based on datestamp of files in emmax-beta-src.tar.gz +# (last checked on 13 Aug 2024) +version = '20100310' + +homepage = 'https://csg.sph.umich.edu//kang/emmax' +description = """EMMAX is a statistical test for large scale human or model organism + association mapping accounting for the sample structure""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://csg.sph.umich.edu//kang/emmax/download/'] +sources = [{'download_filename': 'emmax-beta-src.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['EMMAX-20100310_fix-build.patch'] +checksums = [ + {'EMMAX-20100310.tar.gz': '79670917a0ac74ff1899fb27361e2e07b0f3a7911a9d9c6e0c18cf066b8987ea'}, + {'EMMAX-20100310_fix-build.patch': 'fae62d1f9f7bd4b94c81cdeb01d5134cc2825bcab050ddbfa89ce232eca8497e'}, +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +buildopts = 'CC="$CC $CFLAGS" CLIBS="-lflexiblas -lm -lz"' + +files_to_copy = [(['emmax', 'emmax-kin'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/emmax', 'bin/emmax-kin'], + 'dirs': [], +} + +sanity_check_commands = [ + "emmax 2>&1 | grep '^Usage: emmax'", + "emmax-kin 2>&1 | grep '^Usage: emmax_IBS_kin'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch new file mode 100644 index 00000000000..c2827ab10a9 --- /dev/null +++ b/easybuild/easyconfigs/e/EMMAX/EMMAX-20100310_fix-build.patch @@ -0,0 +1,88 @@ +fix build with recent compiler & BLAS/LAPACK library +author: Kenneth Hoste (HPC-UGent) + +--- emmax-beta-src/emmax.c.orig 2024-08-13 16:28:41.536119000 +0200 ++++ emmax-beta-src/emmax.c 2024-08-13 16:54:06.856501202 +0200 +@@ -7,7 +7,8 @@ + #include + #include + #include +-#include ++#include ++#include + #include + //#include "lapack_wrapper.h" + +@@ -1621,15 +1622,13 @@ + double *W, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevd_ (char *JOBZp, char *UPLOp, int *Np, +- double *A, int *LDAp, +- double *W, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevd_ (&JOBZ, &UPLO, &N, A, &LDA, ++ int32_t N32 = N; ++ int32_t LDA32 = LDA; ++ int32_t LWORK32 = LWORK; ++ dsyevd_ (&JOBZ, &UPLO, &N32, A, &LDA32, + W, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ WORK, &LWORK32, IWORK, &LIWORK, &INFO, 1, 1); + + return INFO; + } +@@ -1640,16 +1639,11 @@ + double *W, double *Z, int LDZ, int *ISUPPZ, + double *WORK, int LWORK, int *IWORK, int LIWORK) + { +- extern void dsyevr_ (char *JOBZp, char *RANGEp, char *UPLOp, int *Np, +- double *A, int *LDAp, double *VLp, double *VUp, +- int *ILp, int *IUp, double *ABSTOLp, int *Mp, +- double *W, double *Z, int *LDZp, int *ISUPPZ, +- double *WORK, int *LWORKp, int *IWORK, int *LIWORKp, +- int *INFOp); + int INFO; +- dsyevr_ (&JOBZ, &RANGE, &UPLO, &N, A, &LDA, &VL, &VU, +- &IL, &IU, &ABSTOL, M, W, Z, &LDZ, ISUPPZ, +- WORK, &LWORK, IWORK, &LIWORK, &INFO); ++ int32_t N32 = N, LDA32 = LDA, IL32 = IL, IU32 = IU, LDZ32 = LDZ, LWORK32 = LWORK, LIWORK32 = LIWORK; ++ dsyevr_ (&JOBZ, &RANGE, &UPLO, &N32, A, &LDA32, &VL, &VU, ++ &IL32, &IU32, &ABSTOL, M, W, Z, &LDZ32, ISUPPZ, ++ WORK, &LWORK32, IWORK, &LIWORK32, &INFO, 1, 1, 1); + + return INFO; + } +@@ -1739,16 +1733,27 @@ + } + + /* Turn Y into its LU form, store pivot matrix */ +- info = clapack_dgetrf (CblasColMajor, n, n, Y, n, ipiv); ++ dgetrf_(&n, &n, Y, &n, ipiv, &info); + + /* Don't bother continuing when illegal argument (info<0) or singularity (info>0) occurs */ +- if (info!=0) return info; ++ if (info != 0) { ++ free(ipiv); ++ return info; ++ } + + /* Feed this to the lapack inversion routine. */ +- info = clapack_dgetri (CblasColMajor, n, Y, n, ipiv); ++ int lwork = n * n; ++ double *work = malloc(lwork * sizeof(double)); ++ if (work == NULL) { ++ printf("malloc failed for work array in matrix_invert\n"); ++ free(ipiv); ++ return 2; ++ } ++ dgetri_(&n, Y, &n, ipiv, work, &lwork, &info); + + /* Cleanup and exit */ + free(ipiv); ++ free(work); + return info; + } + diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb new file mode 100644 index 00000000000..8b461b544cc --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +use_pip = True +sanity_pip_check = True + +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('fair-esm', version, { + 'modulename': "esm, esm.pretrained", + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1382c12efc6 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb new file mode 100644 index 00000000000..60125c1af46 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'ESM3' +version = '3.0.0.post2' + +homepage = 'https://www.evolutionaryscale.ai/' +description = """ESM3 is a frontier generative model for biology, able to jointly reason across +three fundamental biological properties of proteins: sequence, structure, and +function. These three data modalities are represented as tracks of discrete +tokens at the input and output of ESM3. You can present the model with a +combination of partial inputs across the tracks, and ESM3 will provide output +predictions for all the tracks. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch-bundle', '2.1.2'), + ('Transformers', '4.39.3'), + ('Biopython', '1.83'), + ('Biotite', '0.41.0'), + ('Brotli-python', '1.0.9'), + ('einops', '0.7.0'), + ('IPython', '8.14.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('cloudpathlib', '0.16.0', { + 'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'], + }), + ('esm', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import esm'", + "python -c 'from esm.models.esm3 import ESM3'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb new file mode 100644 index 00000000000..4059b342213 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.3.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.3' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/10/a0/e5484d4078f7450042cd7b7a1af24fd3f8d0cb4818f4578e4c322ba488d8/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ee/40/4f6412917f83429f9389b977903c8905f216cb211c8bf3111f28c3017677/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/13/95/44d1e10ceaaf08219ef50d1d97d500ba3b6b34f2d76dd1ff64def71612dc/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.3.tar.gz': '43bbcaa0a7b075eb6483054428ef4b1279a9fc850301171688f86899eaebfff8'}, + {'easybuild_easyblocks-4.9.3.tar.gz': '4f036be918f88fe2dadba87f15d696e9b4d3f8f06986c675b9fafc77b591649d'}, + {'easybuild_easyconfigs-4.9.3.tar.gz': 'f7f501c87cb16a8eb393f5e98cb3cd5f8e84314901e81ff50f8140681b415676'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb new file mode 100644 index 00000000000..13ee3ee70b1 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.4.eb @@ -0,0 +1,56 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.4' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/bd/25/512d9e895a86f4df198274e8a5f6868406d97cc75da9acc5797f78139b52/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/d7/b0/b9289c78fafc21c5c01b225aeee89c69914166742e5f80955d49ed8f9722/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/ed/2c/7b2b22235ffe9310a93cbfef06fb3723466aa8ccc4aca4888b59433e55a6/', +] +# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version +# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_'; +# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358 +sources = [ + { + 'filename': 'easybuild_framework-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s", + }, + { + 'filename': 'easybuild_easyblocks-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s", + }, + { + 'filename': 'easybuild_easyconfigs-%(version)s.tar.gz', + 'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s", + }, +] +checksums = [ + {'easybuild_framework-4.9.4.tar.gz': '5b380a2e3a359f64f06789c390200b922a840f6b10b441e5163696a34bd9bc27'}, + {'easybuild_easyblocks-4.9.4.tar.gz': '1272f1e294090caafde8cbda72ae344ef400fdd161163781f67b3cffe761dd62'}, + {'easybuild_easyconfigs-4.9.4.tar.gz': 'beee4e098f5fee18f2029d6a0b893549aba26e075b147cc0008cb16fd4c8d982'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb new file mode 100644 index 00000000000..c4ae0c4e12d --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2023.07.15-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2023.07.15' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4e57e85a280 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GLib', '2.77.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['share'], +} + +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..97c3992ce77 --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.5-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.8.5' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['aa0c44cab0fffec4c0b3542e91ebcc736b3d41b68a068d30c023ec0df5f93425'] + +builddependencies = [('binutils', '2.42')] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb new file mode 100644 index 00000000000..33fddc6886a --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-iimpi-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['%s -V' % x for x in local_exes if not x.startswith('codes_')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7af581e455f --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.7.0' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e5eb4ef3c7d --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.191-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.191' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['df76db71366d1d708365fc7a6c60ca48398f14367eb2b8954efc8897147ad871'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('binutils', '2.42'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.4'), + ('XZ', '5.4.5'), + ('zstd', '1.5.6'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a70bf3973ca --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.2.1' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb new file mode 100644 index 00000000000..2ed420c412f --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2024a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..246a8306b76 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-7.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '7.0.2' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1ed250407ea8f955cca2f1139da3229fbc13032a0802e4b744be195865ff1541'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('ffnvcodec', '12.2.72.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.03'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('x264', '20240513'), + ('LAME', '3.100'), + ('x265', '3.6'), + ('X11', '20240607'), + ('freetype', '2.13.2'), + ('fontconfig', '2.15.0'), + ('FriBidi', '1.0.15'), + ('SDL2', '2.30.6'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2 --disable-htmlpages' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f767483f7cd --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6c58e69cd22348f441b861092b825e591d0b822e106de6eb0ee4d05d27205b70'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..abb4f293128 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.39')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b44229828a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.40')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..25bf2c570f0 --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.13'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..46b9452f48b --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '3.0.3' + +homepage = 'https://flask.palletsprojects.com/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.2.0', { + 'checksums': ['e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173'], + }), + ('werkzeug', '3.0.4', { + 'checksums': ['34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('blinker', '1.8.2', { + 'checksums': ['8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83'], + }), + ('flask', version, { + 'checksums': ['ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842'], + }), + ('msgspec', '0.18.6', { + 'checksums': ['a59fc3b4fcdb972d09138cb516dbde600c99d07c38fd9372a6ef500d2d031b4e'], + }), + ('Flask-Cors', '5.0.0', { + 'sources': ['flask_cors-%(version)s.tar.gz'], + 'checksums': ['5aadb4b950c4e93745034594d9f3ea6591f734bb3662e16e255ffbf5e89c88ef'], + }), + ('cachelib', '0.13.0', { + 'checksums': ['209d8996e3c57595bee274ff97116d1d73c4980b2fd9a34c7846cd07fd2e1a48'], + }), + ('Flask-Session', '0.8.0', { + 'sources': ['flask_session-%(version)s.tar.gz'], + 'checksums': ['20e045eb01103694e70be4a49f3a80dbb1b57296a22dc6f44bbf3f83ef0742ff'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..4aeb0c7d815 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), + ('Optax', '0.2.2', versionsuffix), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb new file mode 100644 index 00000000000..dedc08531c3 --- /dev/null +++ b/easybuild/easyconfigs/f/Flax/Flax-0.8.4-gfbf-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Flax' +version = '0.8.4' + +homepage = 'https://flax.readthedocs.io' +description = """Flax is a high-performance neural network library and ecosystem for JAX that is +designed for flexibility: Try new forms of training by forking an example and +by modifying the training loop, not by adding features to a framework.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), + ('Optax', '0.2.2'), + ('protobuf-python', '4.24.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('nest_asyncio', '1.6.0', { + 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], + }), + ('orbax_checkpoint', '0.5.15', { + 'modulename': 'orbax.checkpoint', + 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], + }), + ('tensorstore', '0.1.60', { + 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], + }), + ('flax', '0.8.4', { + 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..c11373f69a1 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.4-GCC-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.4' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['197a2dfe39fc324a39d8e1901af4f539609159c4a64a578ec8e60f73f5ea4696'] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8466e596a3d --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + "run_FragGeneScan.pl help", + "run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a31f21a37dd --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.15-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.15' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0bbc7ff633bfa208ae32d7e369cf5a7d20d5d2557a0b067c9aa98bcbf9967587'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..d06d8172e1d --- /dev/null +++ b/easybuild/easyconfigs/f/face-recognition/face-recognition-1.3.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'face-recognition' +version = '1.3.0' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/ageitgey/face_recognition' +description = """Recognize and manipulate faces from Python or from the command line with + the world’s simplest face recognition library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('dlib', '19.24.6', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('face-recognition-models', '0.3.0', { + 'sources': ['face_recognition_models-%(version)s.tar.gz'], + 'checksums': ['b79bd200a88c87c9a9d446c990ae71c5a626d1f3730174e6d570157ff1d896cf'], + }), + (name, version, { + 'sources': ['face_recognition-%(version)s.tar.gz'], + 'checksums': ['5e5efdd1686aa566af0d3cc1313b131e4b197657a8ffd03669e6d3fad92705ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/face_detection', 'bin/face_recognition'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "face_detection --help", + "face_recognition --help", +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb new file mode 100644 index 00000000000..a9d67a03798 --- /dev/null +++ b/easybuild/easyconfigs/f/fastfilters/fastfilters-0.3-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'fastfilters' +version = '0.3' + +homepage = 'https://github.com/ilastik/fastfilters/' +description = """Fast gaussian and derivative convolutional filters.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'optarch': False} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ilastik', + 'repo_name': 'fastfilters', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('pybind11', '2.11.1'), +] + +configopts = '-DFF_INSTALL_DIR="%(installdir)s/lib/python%(pyshortver)s/site-packages/" ' +configopts += '-DPYTHON_EXECUTABLE="$EBROOTPYTHON/bin/python"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib', 'include'], +} + +sanity_check_commands = ["python -c 'import fastfilters'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb new file mode 100644 index 00000000000..49b2a29c4f9 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.13'), + ('libdeflate', '1.19'), + ('ISA-L', '2.31.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb new file mode 100644 index 00000000000..cc4461c3a8b --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.2.72.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.2.72.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0c7e084ac23 --- /dev/null +++ b/easybuild/easyconfigs/f/fish/fish-3.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'fish' + +version = '3.7.1' + +homepage = 'https://fishshell.com/' +description = """ +fish is a smart and user-friendly command line shell for Linux, macOS, and the rest of the family. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/fish-shell/fish-shell/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['614c9f5643cd0799df391395fa6bbc3649427bb839722ce3b114d3bbc1a3b250'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3') +] + +dependencies = [ + ('ncurses', '6.5'), +] + +configopts = '-DBUILD_DOCS=off ' + +sanity_check_paths = { + 'files': ['bin/fish'], + 'dirs': [], +} + +sanity_check_commands = ['fish --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..754eef2c70e --- /dev/null +++ b/easybuild/easyconfigs/f/flash-attention/flash-attention-2.6.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'flash-attention' +version = '2.6.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/Dao-AILab/flash-attention' +description = """Fast and memory-efficient exact attention.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('Ninja', '1.11.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('einops', '0.7.0'), + ('CUTLASS', '3.4.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'flash_attn', + # solves Invalid cross-device link error + # https://github.com/Dao-AILab/flash-attention/issues/875 + 'preinstallopts': "sed -i 's/os.rename/shutil.move/' setup.py && ", + 'source_urls': ['https://github.com/Dao-AILab/flash-attention/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['136e149165d4c8c67273d16daa957b5cd5e6fc629061ffd39fa5a25224454d6c'], + }), +] + +sanity_check_commands = [ + "python -c 'from flash_attn import flash_attn_qkvpacked_func, flash_attn_func'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..6e3bd315965 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..42c0b9a28f1 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-24.3.25-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '24.3.25' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4157c5cacdb59737c5d627e47ac26b140e9ee28b1102f812b36068aab728c1ed'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..d91f13aa5d0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-14.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb index 15b9ad83d78..a19ba324250 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb @@ -17,11 +17,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb index 79b1a625e7e..9ef1de6c8b7 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.4', { diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb index ddc99b99a37..650b15edaa5 100644 --- a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('idna', '3.7', { diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..45cfe72e73f --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.2.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['312151a2d13c8327f5c9c586ac6cf7cddc1658e8f53edae0ec56509c8fa516c9'] + + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8453a35a695 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cfaada6dee8 --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bf71a8f341f --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0e8a62e088b --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed395cfd0ee --- /dev/null +++ b/easybuild/easyconfigs/f/fonttools/fonttools-4.53.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fonttools' +version = '4.53.1' + +homepage = 'https://python-markdown.github.io/' +description = """ +fontTools is a library for manipulating fonts, written in Python. +The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, +which is also called TTX. +It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'fontTools'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/foss/foss-2024a.eb b/easybuild/easyconfigs/f/foss/foss-2024a.eb new file mode 100644 index 00000000000..7e9a4ba5112 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2024a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5184f1f3c1e --- /dev/null +++ b/easybuild/easyconfigs/f/fplll/fplll-5.4.5-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'fplll' +version = '5.4.5' + +homepage = 'https://github.com/fplll/fplll' +description = """fplll contains implementations of several lattice algorithms. + The implementation relies on floating-point orthogonalization, and the 1982 paper from +Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fplll/fplll/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['76d3778f0326597ed7505bab19493a9bf6b73a5c5ca614e8fb82f42105c57d00'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/fplll', 'lib/libfplll.%s' % SHLIB_EXT, 'include/fplll.h'], + 'dirs': ['share'] +} + +sanity_check_commands = ["fplll --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb new file mode 100644 index 00000000000..5361252deb7 --- /dev/null +++ b/easybuild/easyconfigs/f/fpylll/fpylll-0.6.1-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'fpylll' +version = '0.6.1' + +homepage = 'https://pypi.org/project/fpylll' +description = "A Python wrapper for fplll." + +# can be moved down to gfbf in more recent toolchain versions +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dfd9529a26c50993a2a716177debd7994312219070574cad31b35b4f0c040a19'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('cysignals', '1.11.4'), + ('fplll', '5.4.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb new file mode 100644 index 00000000000..6fd245d2079 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.4-foss-2023a.eb @@ -0,0 +1,29 @@ +name = 'GATE' +version = '9.4' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['96c53f6ab1b25c0e540d8f9564bce0049371b378de80a7118a0ff8834c6c117c'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Geant4', '11.2.2'), + ('CLHEP', '2.4.7.1'), + ('ROOT', '6.30.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb new file mode 100644 index 00000000000..7126db6c52d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-14.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.42', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb new file mode 100644 index 00000000000..438a848145f --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-14.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '14.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.3.0.tar.bz2', + 'mpfr-4.2.1.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.4.0.20231231.tar.gz', + {'download_filename': '3136cf9.tar.gz', 'filename': 'nvptx-tools-20240801.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-14.2.0.tar.gz': '7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293'}, + {'gmp-6.3.0.tar.bz2': 'ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'}, + {'mpfr-4.2.1.tar.bz2': 'b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.4.0.20231231.tar.gz': '0c166a39e1bf0951dfafcd68949fe0e4b6d3658081d6282f39aeefc6310f2f13'}, + {'nvptx-tools-20240801.tar.gz': 'a1106bf11b66d12e67194d8aa37196bb96996b614f44b3d3bc1b5854eefec03c'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.42'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index a527795dfc3..576d90e74d6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -63,6 +63,7 @@ _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', '-DPython_ROOT=$EBROOTPYTHON', + '-DGDAL_USE_MYSQL=OFF', ]) # iterative build for both static and shared libraries diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index df1c21eb72a..88e35cd4db4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,7 +61,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb index ba67862143a..21299457516 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.9.0-foss-2023b.eb @@ -60,7 +60,7 @@ dependencies = [ ] # iterative build for both static and shared libraries -local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF " +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DGDAL_USE_MYSQL=OFF " local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " configopts = [ diff --git a/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb new file mode 100644 index 00000000000..d22b6d74689 --- /dev/null +++ b/easybuild/easyconfigs/g/GDMA/GDMA-2.3.3_20230603-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GDMA' +version = '2.3.3_20230603' +_commit = '6b8e81ec' + +homepage = 'https://gitlab.com/anthonyjs/gdma' +description = """ +The GDMA program carries out Distributed Multipole Analysis of wavefunctions +calculated by the Gaussian system of programs or the Psi4 package, using the +formatted checkpoint files that they can produce. The result is a set of +multipole moments at sites defined by the user (usually at the positions of the +atomic nuclei) which, given an accurate wavefunction, provide an accurate +description of the electrostatic field of the molecule.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'source_urls': ['https://gitlab.com/anthonyjs/gdma/-/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['cc008932ae8768e6cbd444337a998e02b2100c123492c260d6020590e76bec1e'] + +parallel = 1 + +skipsteps = ['configure'] + +# avoid using git to obtain the commit: not a cloned repo +prebuildopts = """sed -i "/^log =/,/^commit =/c commit = '%s'" src/version.py && """ % _commit + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' +installopts = 'INSTALL_DIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/gdma'], + 'dirs': [], +} + +sanity_check_commands = ['echo|gdma'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb new file mode 100644 index 00000000000..2074b920ebd --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.10.1-x86_64.eb @@ -0,0 +1,82 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.10.1' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.42'), + ('M4', '1.4.19'), +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +components = [ + ('GMP', '6.3.0', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'], + 'configopts': ' --enable-cxx', + 'start_dir': '%(namelower)s-%(version)s', + }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + 'start_dir': '%(namelower)s-%(version)s', + }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['fab143f10f845629cb1b373309b5680667cbaab298cf49827e383ee8a9ddf683'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb index d098c3c3cbc..4fae7c08b54 100644 --- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -21,11 +21,8 @@ dependencies = [ ('Python-bundle-PyPI', '2023.06'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Markdown', '3.5.2', { diff --git a/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e57a89d030a --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-1.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '1.0.1' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f95eacd4a7b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.80.4-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.80.4' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['24e029c5dfc9b44e4573697adf33078a9827c48938555004b3b9096fa4ea034f'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('libffi', '3.4.5'), + ('gettext', '0.22.5'), + ('libxml2', '2.12.7'), + ('PCRE2', '10.43'), + ('util-linux', '2.40'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb new file mode 100644 index 00000000000..46728a39e63 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.5' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.86.0')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XlsxWriter', '3.1.2'), + ('statsmodels', '0.14.0'), + ('pydot', '2.0.0'), + ('openpyxl', '3.1.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..fbe1458a01a --- /dev/null +++ b/easybuild/easyconfigs/g/GOMC/GOMC-2.76-20230613-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'GOMC' +version = '2.76-20230613' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '9fc85fb' + +homepage = 'https://gomc-wsu.org/' +description = """GPU Optimized Monte Carlo (GOMC) is a parallel molecular +simulation code designed for high-performance simulation of large systems.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/GOMC-WSU/GOMC/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = ['14725836707e4525cc7daea219a6eb47a8aeb675d01ef6d16ad60a9986dd3c1e'] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['6.0', '7.0', '7.5', '8.0', '8.6'] +configopts = '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' + +preinstallopts = 'mkdir %(installdir)s/bin &&' +install_cmd = 'cp' +installopts = '%(builddir)s/easybuild_obj/%(name)s_{CPU,GPU}_* %(installdir)s/bin' + +_gomc_exe = ['GOMC_CPU_GCMC', 'GOMC_CPU_GEMC', 'GOMC_CPU_NPT', 'GOMC_CPU_NVT', 'GOMC_GPU_GCMC', + 'GOMC_GPU_GEMC', 'GOMC_GPU_NPT', 'GOMC_GPU_NVT'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _gomc_exe], + 'dirs': [], +} + +sanity_check_commands = ['%s | grep "Info: GOMC"' % x for x in _gomc_exe] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..83ab6981ae3 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.80.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch'] +checksums = [ + {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'}, + {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch': + 'c1909f1b7fd30784ae789ac0b5e45e0ca3dd2456890b864efa86a2f8c2e563aa'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('Python', '3.12.3'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libffi', '3.4.5'), + ('util-linux', '2.40'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " +configopts = "-Dcairo=enabled" + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch new file mode 100644 index 00000000000..5c09ded1cb2 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch @@ -0,0 +1,52 @@ +This reverts a commit from upstream +> build: Do not install generated GLib GIR files +> +> GLib 2.79 ships its own introspection data. + +However GObject-Introspection requires (optionally) Cairo, which requires GLib +which requires GLib-Introspection for generating the introspection data. + +So there is a cyclic dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517 + +Author: Alexander Grund (TU Dresden) + +diff --git a/gir/meson.build b/gir/meson.build +index 3a016831..312aa886 100644 +--- a/gir/meson.build ++++ b/gir/meson.build +@@ -241,6 +241,8 @@ glib_gir = custom_target('gir-glib', + output: 'GLib-2.0.gir', + depends: [gir_giscanner_pymod, glib_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: glib_command + [ + '--cflags-begin'] + glib_includes + extra_giscanner_cflags + [ +@@ -308,6 +310,8 @@ gobject_gir = custom_target('gir-gobject', + output: 'GObject-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gobject_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gobject_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -360,6 +364,8 @@ uninstalled_gir_files += custom_target('gir-gmodule', + output: 'GModule-2.0.gir', + depends: [glib_gir, gir_giscanner_pymod, gmodule_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gmodule_command + [ + '--include-uninstalled=' + glib_gir.full_path(), +@@ -455,6 +461,8 @@ gio_gir = custom_target('gir-gio', + output: 'Gio-2.0.gir', + depends: [gobject_gir, gir_giscanner_pymod, gio_gir_dep, gdump], + depend_files: gir_giscanner_built_files, ++ install: true, ++ install_dir: girdir, + env: g_ir_scanner_env, + command: gio_command + [ + '--include-uninstalled=' + gobject_gir.full_path(), diff --git a/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb new file mode 100644 index 00000000000..a2a0f0a5adc --- /dev/null +++ b/easybuild/easyconfigs/g/GPflow/GPflow-2.9.2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'GPflow' +version = '2.9.2' + +homepage = 'https://gpflow.github.io' +description = """GPflow is a package for building Gaussian process models in Python. It +implements modern Gaussian process inference for composable kernels and +likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('tensorflow-probability', '0.20.0'), +] + +use_pip = True + +exts_list = [ + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('dropstackframe', '0.1.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['d619c7f87d144660f4569d447648830932f7920d570fd14f0dec552c81a0eb22'], + }), + ('lark', '1.1.9', { + 'checksums': ['15fa5236490824c2c4aba0e22d2d6d823575dcaf4cdd1848e34b6ad836240fba'], + }), + ('check_shapes', '1.1.1', { + 'checksums': ['b699fcb1e60bb17e2c97007e444b89eeeea2a9102ff11d61fb52454af5348403'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('gpflow', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/GPflow/GPflow/archive/'], + 'checksums': ['a32914c2b581b1dd2ac9a6f40352adb5f6f2c32f53028382e542014dd829553e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb new file mode 100644 index 00000000000..ca08a08a88c --- /dev/null +++ b/easybuild/easyconfigs/g/GPyOpt/GPyOpt-1.2.6-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'GPyOpt' +version = '1.2.6' + +homepage = 'https://sheffieldml.github.io/GPyOpt' +description = "GPyOpt is a Python open-source library for Bayesian Optimization" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.6', { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['4916be6f77f457316bcac8460be9c226026aed81fe7be302b32c0ba74e2ac6dd'], + }), + ('GPy', '1.13.2', { + 'modulename': 'GPy', + 'checksums': ['a38256b4dda536a5b5e6134a3924b42d454e987ee801fb6fc8b55a922da27920'], + }), + ('python-dateutil', '2.9.0.post0', { + 'modulename': 'dateutil', + 'checksums': ['37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('sobol-seq', '0.2.0', { + 'sources': ['sobol_seq-%(version)s.tar.gz'], + 'checksums': ['e16e701bd7b03ec6ce65b3a64c9205799f6a2d00c2054dd8c4ff4343f3981172'], + }), + ('emcee', '2.2.1', { + 'checksums': ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'], + }), + (name, version, { + 'modulename': 'GPyOpt', + 'checksums': ['e714daa035bb529a6db23c53665a762a4ab3456b9329c19ad3b03983f94c9b2a'], + }), +] + +local_GPy_file = '%(installdir)s/lib/python%(pyshortver)s/site-packages/GPy/plotting/matplot_dep/plot_definitions.py' + +# Fix GPy with matplotlib>=3.4.0 +# see issue 953 and fix from https://github.com/SheffieldML/GPy/pull/960 +postinstallcmds = [ + 'sed -i ' + '''-e 's|ax._process_unit_info(xdata=X, ydata=y1)|ax._process_unit_info([("x", X), ("y", y1)], convert=False)|' ''' + '''-e 's|ax._process_unit_info(ydata=y2)|ax._process_unit_info([("y", y2)], convert=False)|' %s''' % local_GPy_file, +] + + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb new file mode 100644 index 00000000000..943aa4ac839 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-PLUMED-2.9.0.eb @@ -0,0 +1,100 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +_plumedver = '2.9.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + '%(name)s-%(version)s_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': + '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), + ('PLUMED', _plumedver), +] + + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' + +# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..dd36868a20d --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] +dependencies = [ + ('GLib', '2.80.4'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ac4237f4c0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.11-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.11' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49dcb402388708647e8c321d56b6fb30f21e51e515d0c5a942268d23052a2f00'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('GLib', '2.80.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('X11', '20240607'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb new file mode 100644 index 00000000000..a085843d7d2 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.2.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' +name = 'Geant4-data' +version = '11.2' # version should somewhat match the Geant4 version it should be used in + +homepage = 'https://geant4.web.cern.ch/' +description = """Datasets for Geant4.""" + +toolchain = SYSTEM + +# Pick up the correct sets and versions from cmake/Modules/G4DatasetDefinitions.cmake +# in the Geant source, +# see also https://github.com/Geant4/geant4/blob/v11.2.2/cmake/Modules/G4DatasetDefinitions.cmake +local_datasets = [ + ('G4NDL', '4.7.1', 'G4NDL', 'G4NEUTRONHPDATA'), # NDL + ('G4EMLOW', '8.5', 'G4EMLOW', 'G4LEDATA'), # Low energy electromagnetics + ('PhotonEvaporation', '5.7', 'G4PhotonEvaporation', 'G4LEVELGAMMADATA'), # Photon evaporation + ('RadioactiveDecay', '5.6', 'G4RadioactiveDecay', 'G4RADIOACTIVEDATA'), # Radioisotopes + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS + ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII + ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces + ('G4ABLA', '3.3', 'G4ABLA', 'G4ABLADATA'), # ABLA + ('G4INCL', '1.2', 'G4INCL', 'G4INCLDATA'), # INCL + ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE + ('G4TENDL', '1.4', 'G4TENDL', 'G4PARTICLEHPDATA'), # TENDL +] + +source_urls = ['https://cern.ch/geant4-data/datasets'] +sources = ['%s.%s.tar.gz' % (x[2], x[1]) for x in local_datasets] +checksums = [ + {'G4NDL.4.7.1.tar.gz': 'd3acae48622118d2579de24a54d533fb2416bf0da9dd288f1724df1485a46c7c'}, + {'G4EMLOW.8.5.tar.gz': '66baca49ac5d45e2ac10c125b4fb266225e511803e66981909ce9cd3e9bcef73'}, + {'G4PhotonEvaporation.5.7.tar.gz': '761e42e56ffdde3d9839f9f9d8102607c6b4c0329151ee518206f4ee9e77e7e5'}, + {'G4RadioactiveDecay.5.6.tar.gz': '3886077c9c8e5a98783e6718e1c32567899eeb2dbb33e402d4476bc2fe4f0df1'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, + {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, + {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, + {'G4ABLA.3.3.tar.gz': '1e041b3252ee9cef886d624f753e693303aa32d7e5ef3bba87b34f36d92ea2b1'}, + {'G4INCL.1.2.tar.gz': 'f880b16073ee0a92d7494f3276a6d52d4de1d3677a0d4c7c58700396ed0e1a7e'}, + {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, + {'G4TENDL.1.4.tar.gz': '4b7274020cc8b4ed569b892ef18c2e088edcdb6b66f39d25585ccee25d9721e0'}, +] + +start_dir = '..' + +modextrapaths = {x[3]: x[0] + x[1] for x in local_datasets} + +sanity_check_paths = { + 'files': [], + 'dirs': [x[0] + x[1] for x in local_datasets], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..d4cdf6c78cb --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.2.2-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +name = 'Geant4' +version = '11.2.2' + +homepage = 'https://geant4.web.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = [ + 'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch', +] +checksums = [ + {'geant4-11.2.2.tar.gz': '0b0cfce14e9143079c4440d27ee21f889c4c4172ac5ee7586746b940ffcf812a'}, + {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': + '822265b7cbcaacdffd28b1094786a3c94122aff63338e514d5d3810cdf9218a6'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html + ('CLHEP', '2.4.7.1'), + ('Xerces-C++', '3.2.4'), + ('Qt5', '5.15.10'), + ('Geant4-data', '11.2', '', SYSTEM), +] + +_copts = [ + "-DGEANT4_INSTALL_DATA=OFF", + "-DGEANT4_USE_SYSTEM_ZLIB=ON", + "-DGEANT4_USE_SYSTEM_EXPAT=ON", + "-DGEANT4_USE_SYSTEM_CLHEP=ON", + "-DGEANT4_USE_QT=ON", + "-DGEANT4_USE_GDML=ON", + "-DGEANT4_USE_OPENGL_X11=ON", + "-DGEANT4_USE_RAYTRACER_X11=ON", +] +configopts = ' '.join(_copts) + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb new file mode 100644 index 00000000000..4c6746689d9 --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.7.1' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44'] + +dependencies = [ + ('Python', '3.11.3'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2023.07'), + ('sympy', '1.12'), + ('SPAdes', '3.15.4'), + ('Bowtie2', '2.5.1'), + ('BLAST+', '2.14.1'), + ('Perl', '5.36.1'), + ('matplotlib', '3.7.2') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..174aec3f515 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.03.1-GCCcore-13.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.03.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31cd01682ad23a801cc3bbc222a55f07c4ea3e068bdfb447792d54db21a2e8ad'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.6.2'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('LibTIFF', '4.6.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' + +postinstallcmds = [ + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +sanity_check_commands = ["gs --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e6ca0d7b0aa --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.43-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.43' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('git', '2.45.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('smmap', '5.0.1', {'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62']}), + ('gitdb', '4.0.11', {'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b']}), + (name, version, { + 'modulename': 'git', + 'checksums': ['35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb new file mode 100644 index 00000000000..57a08aeb182 --- /dev/null +++ b/easybuild/easyconfigs/g/Gubbins/Gubbins-3.3.5-foss-2022b.eb @@ -0,0 +1,65 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Gubbins' +version = '3.3.5' + +homepage = "https://nickjcroucher.github.io/gubbins/" +description = """Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that + iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, + while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. + Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term + bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/nickjcroucher/gubbins/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Autoconf-archive', '2023.02.20'), + ('pkgconf', '1.9.3'), + ('Check', '0.15.2'), + ('subunit', '1.4.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('DendroPy', '4.5.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.02'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.6'), + ('rapidNJ', '2.3.3'), + ('RAxML', '8.2.12', '-avx2'), + ('RAxML-NG', '1.2.0'), + ('SKA2', '0.3.7'), + ('dill', '0.3.7'), + ('multiprocess', '0.70.15'), +] + +preconfigopts = "autoreconf -i && " +# runtest = 'check' # runs the Python tests and this causes package to be installed into the Python install +postinstallcmds = [ + """sed -i 's/self.executable = "iqtree"/self.executable = "iqtree2"/' python/gubbins/treebuilders.py""", + "cd python && python -m pip install --prefix %(installdir)s --no-build-isolation . " +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/gubbins', 'lib/libgubbins.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [ + "gubbins --help", + "run_gubbins.py --version", + 'python -c "import gubbins"', + 'python -m pip check', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..06a1dc6a05a --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.14-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.14' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for +the GNU operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8aeb2f353881282fe01694cce76bb72f7ffdd296a12c7a1a39255c27b0dfe5f1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), + ('libtool', '2.4.7'), + ('libreadline', '8.2'), + ('XZ', '5.4.5'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile-%(version_major_minor)s.a", + "include/guile/%(version_major_minor)s/libguile.h"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..46917679856 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.10-GCCcore-13.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.10' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dbdbc97598b2faf31013564efb48e4fed44131d28e996c26abe8a5b23b56c2a'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('gc', '8.2.6'), + ('GMP', '6.3.0'), + ('libffi', '3.4.5'), + ('libunistring', '1.2'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..3a120e6a4e9 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.6-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.6' +local_libatomic_version = '7.8.2' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.6.tar.gz': 'b9183fe49d4c44c7327992f626f8eaa1d8b14de140f243edb1c9dcff7719a7fc'}, + {'libatomic_ops-7.8.2.tar.gz': 'd305207fe207f2b3fb5cb4c019da12b44ce3fcbc593dfd5080d867b1a2419b51'}, +] + +builddependencies = [ + ('binutils', '2.42'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb new file mode 100644 index 00000000000..cb315af1a31 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.3.2-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.3.2' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('wrapt', '1.15.0'), +] + +use_pip = True + +exts_list = [ + ('smart_open', '7.0.4', { + 'checksums': ['62b65852bdd1d1d516839fcb1f6bc50cd0f16e05b4ec44b52f43d38bcb838524'], + }), + (name, version, { + 'checksums': ['99ac6af6ffd40682e70155ed9f92ecbf4384d59fb50af120d343ea5ee1b308ab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb new file mode 100644 index 00000000000..51b74722cb5 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.4.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eba4233b57f --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +builddependencies = [('binutils', '2.40')] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb new file mode 100644 index 00000000000..2b52f3965bc --- /dev/null +++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.13-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'gffutils' +version = '0.13' + +homepage = 'https://github.com/daler/gffutils' +description = """Gffutils is a Python package for working with and manipulating + the GFF and GTF format files typically used for genomic annotations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('pyfaidx', '0.8.1.1'), + ('Biopython', '1.83'), + ('pybedtools', '0.9.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('argh', '0.31.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2edac856ff50126f6e47d884751328c9f466bacbbb6cbfdac322053d94705494'], + }), + ('argcomplete', '3.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d4bcf3ff544f51e16e54228a7ac7f486ed70ebf2ecfe49a63a91171c76bf029b'], + }), + ('simplejson', '3.19.3', { + 'checksums': ['8e086896c36210ab6050f2f9f095a5f1e03c83fa0e7f296d6cba425411364680'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['58e7bb579796fff70e728380ef2d8ffd4a3bc895e53e6529855a0cf87ba6a77a'], + }), +] + +sanity_check_commands = [ + "python -c 'from gffutils import helpers'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..de0ad50b22c --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..66ef70d59ce --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d8db77830fe --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.2' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['be7ffbd057cadebe2aa144542fd90c6838c6a083b5e8a9048b8ee3b66b29d5fb'] + +builddependencies = [ + ('binutils', '2.42'), + ('ImageMagick', '7.1.1-38'), +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2e2696826f6..0e64dba099a 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -16,6 +16,7 @@ dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.38.1', '-nodocs'), + ('libnsl', '2.0.0'), ] sources = [{ @@ -29,7 +30,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 6b6af7f9eba..d21f13320b1 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), + ('libnsl', '2.0.1'), ] sources = [{ @@ -31,7 +32,7 @@ sources = [{ checksums = [None] -prebuildopts = "stack setup && stack build && " +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9701f4ce94d --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240731-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240731' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.45.1'), + ('libnsl', '2.0.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..45d90e26d6a --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.2.0' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e19e62dfeb1e4a57079f0bf51c51dec30633d9fe9e89cb9a083e05e4823afa70'] + +builddependencies = [ + ('binutils', '2.42') +] + +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('MPC', '1.3.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2024a.eb b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb new file mode 100644 index 00000000000..c49f4050ff8 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2024a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2024a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '5.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..16b74bdae1b --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.15.2-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.15.2' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e199ecf26b --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..27e974c5de0 --- /dev/null +++ b/easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'grpcio' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('binutils', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-03-01'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf-python', '4.23.0'), + ('Abseil', '20230125.2'), +] + +exts_list = [ + (name, version, { + 'modulename': 'grpc', + 'preinstallopts': ( + # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined) + "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && " + "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && " + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + 'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&' + "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True " + "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True " + "GRPC_PYTHON_BUILD_SYSTEM_RE2=True " + "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True " + ), + 'patches': ['grpcio-1.57.0_use-ebroot.patch'], + 'checksums': [ + {'grpcio-1.57.0.tar.gz': + '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'}, + {'grpcio-1.57.0_use-ebroot.patch': + '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dd18263d557 --- /dev/null +++ b/easybuild/easyconfigs/g/gtk-doc/gtk-doc-1.34.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'gtk-doc' +version = '1.34.0' + +homepage = 'https://gitlab.gnome.org/GNOME/gtk-doc' +description = """Documentation tool for public library API""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/gtk-doc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1d544fa70ae60014a241b674c9d989f4ad6a96554652ebf73bbe94b4da1aa35'] + +builddependencies = [ + ('binutils', '2.40'), + ('yelp-tools', '42.1'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pygments', '2.18.0'), + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/gtkdoc-depscan', + 'bin/gtkdoc-fixxref', + 'bin/gtkdoc-check', + 'bin/gtkdocize', + 'bin/gtkdoc-mkdb', + 'bin/gtkdoc-mkhtml', + 'bin/gtkdoc-mkhtml2', + 'bin/gtkdoc-mkman', + 'bin/gtkdoc-mkpdf', + 'bin/gtkdoc-rebase', + 'bin/gtkdoc-scan', + 'bin/gtkdoc-scangobj', + ], + 'dirs': [ + 'lib/cmake/GtkDoc', + 'share/%(name)s', + ], +} + +sanity_check_commands = ['gtkdoc-depscan'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb new file mode 100644 index 00000000000..b260708eab8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.38.post1-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.38.post1' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fbdba2ffb5a99a8b52fa2915658ced6bed59f4d0d5f40b1c673646c928aac0b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb index e115932f8ee..3e25fa94133 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-intel-2016a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.11' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24'] builddependencies = [ ('flex', '2.6.0'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb index 36b03f18536..5fade2d2248 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.12-intel-2017a.eb @@ -3,15 +3,16 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.12' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +checksums = ['dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb index f1b4395af48..39dc5507935 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.13' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb index 84bff2749e9..74e44dbfc26 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.13-intel-2017a-no-netcdf.eb @@ -4,7 +4,7 @@ name = 'HDF' version = '4.2.13' versionsuffix = '-no-netcdf' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. This version suppresses the netcdf api, that gives issues with some applications""" @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] checksums = ['be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb index 1f31e675f7a..56e705f36a2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'http://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 204d917a179..51b65acec93 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index bf3fff366f2..a78efd6cee2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index ff08dc71e80..fdee3ff0383 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb index bdb2cb878ee..91e084fc238 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb index 869a6a796a2..7fff3f348bb 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb index fc36bb04673..7acaaafc09d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb index 682e5e20b6c..4af8d274164 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb index f0286cd30bd..abab2d962f5 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index fd6e6693977..7e6b5eefbe8 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.15' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] patches = ['HDF-4.2.15_fix-aarch64.patch'] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index 453ca292d42..175aaba4731 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb index 6f54f50d488..f2c20e888b9 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16-2' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index d24dbfac77e..fd9d8d3d4ea 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.16' -homepage = 'https://www.hdfgroup.org/products/hdf4/' +homepage = 'https://support.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['http://support.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167'] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb index f2aab3663a3..5cb05f4a4a1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb index 77fa0c12ab9..e180d8619ee 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] +patches = ['HDF5-1.14.3_suppress_fp_exceptions.patch'] +checksums = [ + {'hdf5-1.14.3.tar.gz': '09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'}, + {'HDF5-1.14.3_suppress_fp_exceptions.patch': 'bf33e579c93a16043c54b266321bbe95e4a8797f7fe6d096a13ce905ed2ffde7'}, +] # replace src include path with installation dir for $H5BLD_CPPFLAGS _regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch new file mode 100644 index 00000000000..420125db46d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch @@ -0,0 +1,223 @@ +See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +Created using +git checkout hdf5-1_14_3 +git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b + +commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82 +Author: Dana Robinson <43805+derobins@users.noreply.github.com> +Date: Tue Nov 7 08:13:30 2023 -0800 + + Disable FP exceptions in H5T init code (#3837) + + The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. + + Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. + + Fixes #3831 + +diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 +index 328f8d3cec..079f08d96c 100644 +--- a/config/linux-gnulibc1 ++++ b/config/linux-gnulibc1 +@@ -173,10 +173,7 @@ case $FC_BASENAME in + nagfor) + + F9XSUFFIXFLAG="" +- # NOTE: The default is -ieee=stop, which will cause problems +- # when the H5T module performs floating-point type +- # introspection +- AM_FCFLAGS="$AM_FCFLAGS -ieee=full" ++ AM_FCFLAGS="$AM_FCFLAGS" + FSEARCH_DIRS="" + + # Production +diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt +index 200576332b..7de2a56974 100644 +--- a/release_docs/RELEASE.txt ++++ b/release_docs/RELEASE.txt +@@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release + =================================== + Library + ------- ++ - Suppressed floating-point exceptions in H5T init code ++ ++ The floating-point datatype initialization code in H5Tinit_float.c ++ could raise FE_INVALID exceptions while munging bits and performing ++ comparisons that might involve NaN. This was not a problem when the ++ initialization code was executed in H5detect at compile time (prior ++ to 1.14.3), but now that the code is executed at library startup ++ (1.14.3+), these exceptions can be caught by user code, as is the ++ default in the NAG Fortran compiler. ++ ++ Starting in 1.14.4, we now suppress floating-point exceptions while ++ initializing the floating-point types and clear FE_INVALID before ++ restoring the original environment. ++ ++ Fixes GitHub #3831 ++ ++ - Fixed a file handle leak in the core VFD ++ ++ When opening a file with the core VFD and a file image, if the file ++ already exists, the file check would leak the POSIX file handle. ++ ++ Fixes GitHub issue #635 ++ + - Fixed some issues with chunk index metadata not getting read + collectively when collective metadata reads are enabled + +@@ -619,12 +642,6 @@ Known Problems + this release with link errors. As a result, Windows binaries for this release + will not include Fortran. The problem will be addressed in HDF5 1.14.4. + +- IEEE standard arithmetic enables software to raise exceptions such as overflow, +- division by zero, and other illegal operations without interrupting or halting +- the program flow. The HDF5 C library intentionally performs these exceptions. +- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program +- to avoid stopping on an exception. +- + CMake files do not behave correctly with paths containing spaces. + Do not use spaces in paths because the required escaping for handling spaces + results in very complex and fragile build files. +diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c +index 3b9e127fe4..3213f00fec 100644 +--- a/src/H5Tinit_float.c ++++ b/src/H5Tinit_float.c +@@ -51,19 +51,23 @@ + * Function: DETECT_F + * + * Purpose: This macro takes a floating point type like `double' and +- * a base name like `natd' and detects byte order, mantissa +- * location, exponent location, sign bit location, presence or +- * absence of implicit mantissa bit, and exponent bias and +- * initializes a detected_t structure with those properties. ++ * and detects byte order, mantissa location, exponent location, ++ * sign bit location, presence or absence of implicit mantissa ++ * bit, and exponent bias and initializes a detected_t structure ++ * with those properties. ++ * ++ * Note that these operations can raise floating-point ++ * exceptions and building with some compiler options ++ * (especially Fortran) can cause problems. + *------------------------------------------------------------------------- + */ +-#define DETECT_F(TYPE, VAR, INFO) \ ++#define DETECT_F(TYPE, INFO) \ + do { \ +- TYPE _v1, _v2, _v3; \ +- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ +- unsigned char _pad_mask[sizeof(TYPE)]; \ +- unsigned char _byte_mask; \ +- int _i, _j, _last = (-1); \ ++ TYPE _v1, _v2, _v3; \ ++ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ ++ uint8_t _pad_mask[sizeof(TYPE)]; \ ++ uint8_t _byte_mask; \ ++ int _i, _j, _last = -1; \ + \ + memset(&INFO, 0, sizeof(INFO)); \ + INFO.size = sizeof(TYPE); \ +@@ -81,7 +85,7 @@ + _v1 = (TYPE)4.0L; \ + H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \ + for (_i = 0; _i < (int)sizeof(TYPE); _i++) \ +- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \ ++ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \ + _buf1[_i] ^= _byte_mask; \ + H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \ + H5_GCC_CLANG_DIAG_OFF("float-equal") \ +@@ -118,7 +122,7 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)-1.0L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \ + \ + /* Mantissa */ \ + INFO.mpos = 0; \ +@@ -126,12 +130,11 @@ + _v1 = (TYPE)1.0L; \ + _v2 = (TYPE)1.5L; \ + if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \ +- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ ++ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \ + INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \ + \ + /* Exponent */ \ +- INFO.epos = INFO.mpos + INFO.msize; \ +- \ ++ INFO.epos = INFO.mpos + INFO.msize; \ + INFO.esize = INFO.sign - INFO.epos; \ + \ + _v1 = (TYPE)1.0L; \ +@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d) + herr_t H5_NO_UBSAN + H5T__init_native_float_types(void) + { ++ fenv_t saved_fenv; + H5T_fpoint_det_t det; + H5T_t *dt = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_PACKAGE + ++ /* Turn off floating-point exceptions while initializing to avoid ++ * tripping over signaling NaNs while looking at "don't care" bits. ++ */ ++ if (feholdexcept(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment"); ++ + /* H5T_NATIVE_FLOAT */ + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(float, FLOAT, det); ++ DETECT_F(float, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -497,7 +507,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(double, DOUBLE, det); ++ DETECT_F(double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -528,7 +538,7 @@ H5T__init_native_float_types(void) + + /* Get the type's characteristics */ + memset(&det, 0, sizeof(H5T_fpoint_det_t)); +- DETECT_F(long double, LDOUBLE, det); ++ DETECT_F(long double, det); + + /* Allocate and fill type structure */ + if (NULL == (dt = H5T__alloc())) +@@ -561,6 +571,14 @@ H5T__init_native_float_types(void) + H5T_native_order_g = det.order; + + done: ++ /* Clear any FE_INVALID exceptions from NaN handling */ ++ if (feclearexcept(FE_INVALID) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions"); ++ ++ /* Restore the original environment */ ++ if (feupdateenv(&saved_fenv) != 0) ++ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment"); ++ + if (ret_value < 0) { + if (dt != NULL) { + dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); +diff --git a/src/H5private.h b/src/H5private.h +index 14a0ac3225..3aaa0d5245 100644 +--- a/src/H5private.h ++++ b/src/H5private.h +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb new file mode 100644 index 00000000000..a4057965c49 --- /dev/null +++ b/easybuild/easyconfigs/h/HERRO/HERRO-0.1.0_20240808-foss-2023a.eb @@ -0,0 +1,382 @@ +easyblock = 'Cargo' + +name = 'HERRO' +version = '0.1.0_20240808' +local_commit = 'deccc46' + +homepage = 'https://github.com/lbcb-sci/herro' +description = """ +HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or +R9.4.1 reads (read length of >= 10 kbps is recommended). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/lbcb-sci/herro/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('bzip2', '1.0.8'), + ('libffi', '3.4.4'), + ('libnsl', '2.0.1'), + ('SQLite', '3.42.0'), + ('util-linux', '2.39'), + ('zlib', '1.2.13'), + ('ncurses', '6.4'), + ('libreadline', '8.2'), + ('SeqKit', '2.3.1', '', SYSTEM), + ('Tk', '8.6.13'), + ('XZ', '5.4.2'), + ('matplotlib', '3.7.2'), + ('edlib', '1.3.9'), + ('h5py', '3.9.0'), + ('duplex-tools', '0.3.3'), + ('PyTorch', '2.1.2'), + ('Pillow', '10.0.0'), + ('zstd', '1.5.5'), + ('parasail', '2.6.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('zstandard', '0.22.0', { + 'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'], + }), + ('Porechop', '20240119', { + 'modulename': 'porechop', + 'source_urls': ['https://github.com/dehui333/Porechop/archive/'], + 'sources': [{'download_filename': 'd2e77c6.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'], + }), +] + +# use tch version 0.14.0 - compatible with PyTorch 2.1 +local_torch_opts = "sed -i 's/tch = \"0.13.0\"/tch = \"0.14.0\"/' Cargo.toml && " +local_torch_opts += 'export LIBTORCH_BYPASS_VERSION_CHECK=1 && export LIBTORCH_USE_PYTORCH=1 && ' +local_torch_opts += 'export LIBTORCH=$EBROOTPYTORCH/lib && RUSTFLAGS="-Ctarget-cpu=native"' +prebuildopts = pretestopts = preinstallopts = local_torch_opts + +# copy scripts to /bin to be easier to run scripts for users +postinstallcmds = [ + 'cp -a %(start_dir)s/scripts/* %(installdir)s/bin', + 'rm %(installdir)s/bin/herro-env.yml', + "chmod a+rx %(installdir)s/bin/*.sh", + "chmod a-x %(installdir)s/bin/*.py", +] + +_bins = [ + 'herro', + 'porechop', + 'no_split.sh', + 'postprocess_corrected.sh', + 'create_batched_alignments.sh', + 'porechop_with_split.sh', + 'preprocess.sh', + 'batch.py', + 'create_clusters.py', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["herro --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +modloadmsg = """ +To run scripts from /scripts directory just run .sh +Do not run it as scripts/.sh +For example - run preprocess.sh as: + $ preprocess.sh +""" + +crates = [ + ('adler2', '2.0.0'), + ('aes', '0.8.4'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('anyhow', '1.0.86'), + ('approx', '0.5.1'), + ('autocfg', '1.3.0'), + ('base64ct', '1.6.0'), + ('block-buffer', '0.10.4'), + ('buffer-redux', '1.0.2'), + ('bytecount', '0.6.8'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('cipher', '0.4.4'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('colorchoice', '1.0.2'), + ('console', '0.15.8'), + ('constant_time_eq', '0.1.5'), + ('cpufeatures', '0.2.13'), + ('crc32fast', '1.4.2'), + ('crossbeam-channel', '0.5.13'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('crypto-common', '0.1.6'), + ('deranged', '0.3.11'), + ('digest', '0.10.7'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('flate2', '1.0.32'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hmac', '0.12.1'), + ('indicatif', '0.17.8'), + ('inout', '0.1.3'), + ('instant', '0.1.13'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jemalloc-sys', '0.5.4+5.3.0-patched'), + ('jemallocator', '0.5.4'), + ('jobserver', '0.1.32'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.158'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.9'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.8.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('npyz', '0.8.3'), + ('npyz-derive', '0.7.0'), + ('num-bigint', '0.4.6'), + ('num-complex', '0.4.6'), + ('num-conv', '0.1.0'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.19'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.19.0'), + ('ordered-float', '4.2.2'), + ('password-hash', '0.4.2'), + ('pbkdf2', '0.11.0'), + ('pest', '2.7.11'), + ('pest_derive', '2.7.11'), + ('pest_generator', '2.7.11'), + ('pest_meta', '2.7.11'), + ('pkg-config', '0.3.30'), + ('portable-atomic', '1.7.0'), + ('powerfmt', '0.2.0'), + 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'a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261'}, + {'time-0.3.36.tar.gz': '5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885'}, + {'time-core-0.1.2.tar.gz': 'ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3'}, + {'torch-sys-0.14.0.tar.gz': '803446f89fb877a117503dbfb8375b6a29fa8b0e0f44810fac3863c798ecef22'}, + {'typenum-1.17.0.tar.gz': '42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825'}, + {'ucd-trie-0.1.6.tar.gz': 'ed646292ffc8188ef8ea4d1e0e0150fb15a5c2e12ad9b8fc191ae7a8a7f3c4b9'}, + {'unicode-ident-1.0.12.tar.gz': '3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b'}, + {'unicode-width-0.1.13.tar.gz': '0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d'}, + {'utf8parse-0.2.2.tar.gz': '06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821'}, + {'version_check-0.9.5.tar.gz': '0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, + {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb new file mode 100644 index 00000000000..bb76dc1e937 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023b.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb similarity index 94% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb index ca7fc54ce2f..8a70a42bb41 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024.06.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2024a.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2024.06'} +toolchain = {'name': 'foss', 'version': '2024a'} toolchainopts = {'usempi': True} source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb new file mode 100644 index 00000000000..5544839d177 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2024a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..40540c3fcdc --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'HarfBuzz' +version = '9.0.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['HarfBuzz-9.0.0_fix-subset-test.patch'] +checksums = [ + {'9.0.0.tar.gz': 'b7e481b109d19aefdba31e9f5888aa0cdfbe7608fed9a43494c060ce1f8a34d2'}, + {'HarfBuzz-9.0.0_fix-subset-test.patch': '1635505c27c312dca507863f2a865eb88d42e35ff4cc241cfa0e90c0ade8b790'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), + ('fonttools', '4.53.1'), # For tests +] + +dependencies = [ + ('GLib', '2.80.4'), + ('ICU', '75.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +configopts = '--default-library=both' # static and shared library +configopts += ' -Dgobject=enabled -Dintrospection=enabled' +configopts += ' -Dglib=enabled' +configopts += ' -Dicu=enabled' +configopts += ' -Dcairo=enabled' +configopts += ' -Dfreetype=enabled' + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch new file mode 100644 index 00000000000..25a2b619fc8 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-9.0.0_fix-subset-test.patch @@ -0,0 +1,26 @@ +The test "feature_variation_instance_collect_lookups" fails when run in environments +where the decimal separator is not a dot ("."). +Fix this by using the C locale. +See https://github.com/harfbuzz/harfbuzz/pull/4857 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/subset/run-tests.py b/test/subset/run-tests.py +index 9e09d95d1d9..c0c256d8974 100755 +--- a/test/subset/run-tests.py ++++ b/test/subset/run-tests.py +@@ -135,10 +135,13 @@ def check_ots (path): + + has_ots = has_ots() + ++env = os.environ.copy() ++env['LC_ALL'] = 'C' + process = subprocess.Popen ([hb_subset, '--batch'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, +- stderr=sys.stdout) ++ stderr=sys.stdout, ++ env=env) + + fails = 0 + for path in args: diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb index a05239847d3..993087b828c 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -12,7 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] +patches = ['Highway-1.0.4-zen4-fix-TruncateTo-bug.patch'] + +checksums = [ + {'1.0.4.tar.gz': 'faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'}, + {'Highway-1.0.4-zen4-fix-TruncateTo-bug.patch': + 'e571413c290076a729dbb1df105a4bfa106099238d1b438e74a9dfc9557eb4a2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch new file mode 100644 index 00000000000..f489a6bd15f --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-zen4-fix-TruncateTo-bug.patch @@ -0,0 +1,59 @@ +A single test failed when building on AMD Genoa a.k.a Zen4 with the error message +reported in https://github.com/google/highway/issues/1913 + +Building v1.0.5 passed all tests. Hence, this patch uses some of the changes made +in v1.0.5 to let the single failing test succeed. + +Looking at the PRs added by v1.0.5 a promising candidate was identified +(https://github.com/google/highway/pull/1276) and all changed files in the PR +were "studied in detail" (assessed if the changes could be related to the failing +test on Zen4). Luckily, the four changes provided in the patch below were +found to resolve the issue. It was also tested if a subset of these four changes +would resolve the issue, but this did not succeed. + +Author: Thomas Roeblitz (University of Bergen) + +diff --git a/hwy/ops/x86_256-inl.h b/hwy/ops/x86_256-inl.h +index 4e2e83e8..2fbf99c7 100644 +--- a/hwy/ops/x86_256-inl.h ++++ b/hwy/ops/x86_256-inl.h +@@ -4185,7 +4185,7 @@ HWY_INLINE Vec128 LookupAndConcatHalves(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = { + LO, HI, 0x10101010 + LO, 0x10101010 + HI, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + #else + alignas(32) static constexpr uint32_t kMap[8] = {LO, HI, ~0u, ~0u, + ~0u, ~0u, LO, HI}; +@@ -4208,7 +4208,7 @@ HWY_INLINE Vec128 LookupAndConcatQuarters(Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint16_t kMap[16] = { + LO, HI, 0x1010 + LO, 0x1010 + HI, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d16, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d16, kMap).raw, v.raw); + return LowerHalf(Vec128{_mm256_castsi256_si128(result)}); + #else + constexpr uint16_t ff = static_cast(~0u); +@@ -4229,7 +4229,7 @@ HWY_API Vec32 TruncateTo(D /* tag */, Vec256 v) { + #if HWY_TARGET <= HWY_AVX3_DL + alignas(32) static constexpr uint32_t kMap[8] = {0x18100800u, 0, 0, 0, + 0, 0, 0, 0}; +- const auto result = _mm256_permutexvar_epi8(v.raw, Load(d32, kMap).raw); ++ const auto result = _mm256_permutexvar_epi8(Load(d32, kMap).raw, v.raw); + return LowerHalf(LowerHalf(LowerHalf(Vec256{result}))); + #else + alignas(32) static constexpr uint32_t kMap[8] = {0xFFFF0800u, ~0u, ~0u, ~0u, +diff --git a/hwy/ops/x86_512-inl.h b/hwy/ops/x86_512-inl.h +index 167922d8..83f2ee67 100644 +--- a/hwy/ops/x86_512-inl.h ++++ b/hwy/ops/x86_512-inl.h +@@ -3497,7 +3497,7 @@ HWY_API Vec128 TruncateTo(D /* tag */, const Vec512 v) { + alignas(16) static constexpr uint8_t k8From32[16] = { + 0, 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60}; + const Vec512 bytes{ +- _mm512_permutexvar_epi32(LoadDup128(d8, k8From32).raw, v.raw)}; ++ _mm512_permutexvar_epi8(LoadDup128(d8, k8From32).raw, v.raw)}; + #else + const Full512 d32; + // In each 128 bit block, gather the lower byte of 4 uint32_t lanes into the diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..27739befe52 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.2.0' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7e0be78b8318e8bdbf6fa545d2ecb4c90f947df03f7aadc42c1967f019e63343'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb index 0b79b7cfc94..605d20f196f 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-foss-2018b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb index 81636ad6de3..079d5eb7de1 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2019b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb index 8e8e8c7f705..50fe19e455a 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.3' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +source_urls = ['http://support.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb index 1a825bc8ed8..28d67776a1b 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'h4toh5' version = '2.2.5' -homepage = 'http://www.hdfgroup.org/h4toh5/' +homepage = "https://docs.hdfgroup.org/archive/support/products/hdf5_tools/h4toh5/index.html" description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..2161ee0b1af --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-14.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.42', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..bc3a5a1c715 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb new file mode 100644 index 00000000000..f2072785aa5 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.2-Julia-1.10.3.eb @@ -0,0 +1,84 @@ +easyblock = 'JuliaBundle' + +name = 'IJulia' +version = '1.24.2' +_julia_ver = '1.10.3' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_list = [ + ('Preferences', '1.4.3', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['02b995891818b91266f98bcb46eefc513dfb66b177b5a6a0d1cff97be3e4582d'], + }), + ('JLLWrappers', '1.5.0', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['6e83b81afd0c57636e80bcf52ad51f6ba43d98643cac999727b958d9ab3d4a01'], + }), + ('SnoopPrecompile', '2.10.8', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['9b3204ce72fa3d0f1a359428e9f2ae43db2ee91f7ba77407056aced39d74d9d6'], + }), + ('PrecompileTools', '1.2.1', { + 'source_urls': ['https://github.com/JuliaLang/PrecompileTools.jl/archive/'], + 'checksums': ['af58b384e08b488b2da5ad19e72817b8b0ddb026997f8cf85f2964cc2c26cd34'], + }), + ('Parsers', '2.8.1', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['6ea035be48ef5daaecdff62ac8f29c6110aaf20f3349058a4f96e2503f55b693'], + }), + ('JSON', '0.21.4', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['c6b620ad4150ec5a154367f50c9579af800e3a89a6d8f9cb5dd30215a5d3f552'], + }), + ('MbedTLS', '1.1.9', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['d421bb36f9eb7f8840bd7108c2c33a9a5532454ac9465861e2f7797f89c1f56b'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.10.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2007170cad58d6f27626500abd52bd782023b8ecb7a7d05a678d7aec3c0f9948'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['29d1f35e48c1436743a6da28518cb7aeccb32af4b439c3976df1967c6a252e87'], + }), + ('ZMQ', '1.2.4', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['a15fe752d2b049ad7521d03909ae8ad6c28e4cf46fc823f666cbc1cc6f5795ba'], + }), + (name, version, { + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['de215348c7c41e1ca15c0d21f5f9a78bedce77b02ef89d67f38702c4d57ee80d'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1e79d2b10db --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.31.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e218b7b2e241cfb8e8b68f54a6e5eed80968cc387c4b1af03708b54e9fb236f1'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [('NASM', '2.16.03')] + +preconfigopts = "autoreconf -i -f &&" + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb new file mode 100644 index 00000000000..9ba65978898 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb @@ -0,0 +1,78 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak, Pavel Tománek (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.3.0' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ITK-5.3.0_vtk-include.patch', + 'ITK-5.3.0_fix-compatibility-swig-4-1.patch', +] +checksums = [ + {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'}, + {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'}, + {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), + ('SWIG', '4.1.1'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('Python', '3.10.8'), + ('double-conversion', '3.2.1'), + ('expat', '2.4.9'), + ('HDF5', '1.14.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('VTK', '9.2.6'), + ('zlib', '1.2.12'), +] + +# Features +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +# Enable Python bindings +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG ' +configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +# Dependencies from EB +local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch new file mode 100644 index 00000000000..f77306c9f8e --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch @@ -0,0 +1,13 @@ +Manually add the include directory of VTK +dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375 +author: Alex Domingo (Vrije Universiteit Brussel) +--- Wrapping/CMakeLists.txt.orig 2023-12-21 13:41:44.845008000 +0100 ++++ Wrapping/CMakeLists.txt 2023-12-21 13:42:14.794328946 +0100 +@@ -112,6 +112,7 @@ + ############################################################################### + # Configure specific wrapper modules + ############################################################################### ++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/") + + unset(WRAP_ITK_MODULES CACHE) + \ No newline at end of file diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..776471b14b2 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-38' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['ImageMagick-7.1.1-38_fix-linking.patch'] +checksums = [ + {'7.1.1-38.tar.gz': '5e449530ccec8b85ae2bfd1ad773184fb7a4737d40fd9439db8a5d4beee4403e'}, + {'ImageMagick-7.1.1-38_fix-linking.patch': '0fbe8e3b6621e3e0d1efec59949fecb45924bc6e65851b9b6399bb3eff8d55d9'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20240607'), + ('Ghostscript', '10.03.1'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('LibTIFF', '4.6.0'), + ('LittleCMS', '2.16'), + ('Pango', '1.54.0'), + ('pixman', '0.43.4'), + ('FriBidi', '1.0.15'), +] + +preconfigopts = 'PKG_CONFIG=$EBROOTPKGCONF/bin/pkgconf' +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': ['bin/magick'], + 'dirs': ['etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +sanity_check_commands = [ + 'magick --help', +] + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch new file mode 100644 index 00000000000..2c9d54a4ac0 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-38_fix-linking.patch @@ -0,0 +1,27 @@ +The configure script sets this to a path inside the install location which is empty during build. +However this path(s) is/are used by the compiler/linker to find libraries. `pkg-config` used during configure assumes this is the same during build as on invocation of itself and omits any path already contained in the variable. + +This combination causes build failures due to dependent libraries not being found in the link step unless there happens to be some other way the paths get pulled in. E.g. if HarfBuzz is built using (the deprecated) configure&make it has `*.la` files which contain the required link flags. If HarfBuzz is built using the new Meson build system those files are no longer present and the linker paths will be missing. + +As there doesn't seem to be a specific reason for the variable to be set to an empty directory in the Makefile just remove it. + +See https://github.com/ImageMagick/ImageMagick/pull/7613 + +Author: Alexander Grund (TU Dresden) + +--- + Makefile.in | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/Makefile.in b/Makefile.in +index 47b78566f0c..3a9761cfd5b 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -3288,7 +3288,6 @@ LIBOBJS = @LIBOBJS@ + LIBOPENJP2_CFLAGS = @LIBOPENJP2_CFLAGS@ + LIBOPENJP2_LIBS = @LIBOPENJP2_LIBS@ + LIBRARY_EXTRA_CPPFLAGS = @LIBRARY_EXTRA_CPPFLAGS@ +-LIBRARY_PATH = @LIBRARY_PATH@ + LIBS = @LIBS@ + LIBSTDCLDFLAGS = @LIBSTDCLDFLAGS@ + LIBTOOL = @LIBTOOL@ diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..05efb6d6c62 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.11' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057849585e49b8b85abe7cc1e76e22963b01bfdc3b6d83eac90c499cd760063'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb index b27635916ca..179e26005de 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel Inspector XE is an easy to use memory error checker and t toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15827/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15827/'] sources = ['inspector_%(version)s.tar.gz'] checksums = ['676fd0b25a56fba63495c048abf485b08583cbb01eb0cf6e1174ee7b352af6d5'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb index 11b56c0bc1c..494b031a5e1 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18239/'] sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh'] checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb index 430cc62b2d4..22f082dd1f4 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18363/'] sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb index a7772259cc8..33515e7a8e5 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb @@ -10,7 +10,7 @@ description = """Intel Inspector is a dynamic memory and threading error toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18712/'] sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh'] checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e'] diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb index 55107c33e8a..c0357dea2d0 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -13,7 +13,7 @@ can be identified and practical resolutions provided. toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18359/'] sources = ['l_clck_p_%(version)s.560_offline.sh'] checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index c46f42bb81b..48ab0a8f836 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index fd51e3b2082..d0c2dc13c67 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (local_pysver, local_relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb new file mode 100644 index 00000000000..41248bcbf73 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.5.0-foss-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'IsoQuant' +version = '3.5.0' + +homepage = 'https://github.com/ablab/IsoQuant' +description = """IsoQuant is a tool for the genome-based analysis of long RNA reads, + such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify + transcript models with high precision and decent recall. If the reference annotation is given, + IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. + IsoQuant further performs annotated gene, isoform, exon and intron quantification. + If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/ablab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['8cbba80b5eb0ed85fe0b519693157eb97820bc1d79ff44435736bf799af85c1f'] + +dependencies = [ + ('Python', '3.11.3'), + ('gffutils', '0.13'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('Pysam', '0.22.0'), + ('pyfaidx', '0.8.1.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.18'), + ('PyYAML', '6.0'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['isoquant.py'], + 'dirs': [], +} + +sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index ca49a084587..f6eb99cebdc 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ddbfdf88eed095817650ec0a226ef3b9c07c41c855d258e80eaade5173fedb6e'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index 9b3a071f005..c04b1a09909 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['d8b7e6633faa2e0b7d4eebf3260cb3a200b951cb2cf7b5db957c5ae71508d34b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 3918ba3f3f1..f2d6c096878 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_cpp.tgz'] checksums = ['3850ab2a01fe8888af8fed65b7d24e0ddf45a84efe9635ff0f118c38dfc4544b'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index b78d2e8e11c..5cf05e6a559 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] checksums = ['17932a54a76d04432de16e6db15a6ed80fa80ed20193f3b717fd391f623e23e1'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 7b37d3169dc..f2341a844c3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['4a156bbeac9bd8d67e74b33ad6f3ae02d4c24c8444365465db6dc50d3e891946'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index f192fd17472..9f9b71a21df 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 65821a417db..2d194db100a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel C and C++ compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb index 5cefbfc2dee..85453f37251 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.4.243.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15537/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb index c080762f21d..b4eb6588ec7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15813/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb index a8f9c94588f..a21e15527d5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb index 70593480c69..4ad42c13a31 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.0.166.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16229/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb index 89d42319787..98e64dff918 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16530/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb index fbd8bc1719b..056539c7f76 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel C, C++ & Fortran compilers" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17117/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17117/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 66cf55bd0c0..2ce7d5ee7f1 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 8572f079dca..3bdc51210af 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 7668ec76749..3f9f1de0c45 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template sources = ['parallel_studio_xe_%(version_major)s_update4_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 3457239087d..453cf476095 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index c47117b085b..c6c03d9340f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 924762c6de2..5a043c03822 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index b8eb911adc2..b996c679995 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel Fortran compiler" toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] checksums = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb similarity index 95% rename from easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb index 82db31cd099..d6150133621 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2024a.eb @@ -2,7 +2,7 @@ easyblock = 'Toolchain' name = 'iimpi' -version = '2024.06' +version = '2024a' homepage = 'https://software.intel.com/parallel-studio-xe' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb new file mode 100644 index 00000000000..64e20f93f38 --- /dev/null +++ b/easybuild/easyconfigs/i/ilastik-napari/ilastik-napari-0.2.4-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ilastik-napari' +version = '0.2.4' + +homepage = 'https://github.com/ilastik/ilastik-napari/' +description = "Napari plugin for interactive pixel classification." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('QtPy', '2.4.1'), + ('scikit-learn', '1.3.1'), + ('numba', '0.58.1'), + ('fastfilters', '0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sparse', '0.15.4', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['76ec76fee2aee82a84eb97155dd530a9644e3b1fdea2406bc4b454698b36d938'], + }), + (name, version, { + 'source_tmpl': 'ilastik_napari-%(version)s.tar.gz', + 'modulename': 'ilastik', + 'checksums': ['8e971a70389f9257eaca7561637301f996f316fdff2cb223c5828d162970bec4'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb similarity index 84% rename from easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb rename to easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb index 7984030b590..b26ab65f452 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024.06.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2024.2.0-iimpi-2024a.eb @@ -4,7 +4,7 @@ version = '2024.2.0' homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' description = "FFTW interfaces using Intel oneAPI Math Kernel Library" -toolchain = {'name': 'iimpi', 'version': '2024.06'} +toolchain = {'name': 'iimpi', 'version': '2024a'} dependencies = [('imkl', version, '', SYSTEM)] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb index 65486c1a522..1af220dba70 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28-serial.eb @@ -12,7 +12,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb index 770acb76d87..a90fc9aaaac 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.1.163-iimpi-2018a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12384/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12384/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6dc263fc6f3c350979740a13de1b1e8745d9ba0d0f067ece503483b9189c2ca'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb index f340d755ee2..c873144967b 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 6ead35efc9a..89a3f33d184 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb index 7f53145d6a3..450dc0082e2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iimpi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb index aeabee4d300..0fcf2f60e8e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-iompi-2018b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2018b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb index 02dba60737e..7d2dc1809af 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.4.274-iimpi-2018.04.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2018.04'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13725/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13725/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['18eb3cde3e6a61a88f25afff25df762a560013f650aaf363f7d3d516a0d04881'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb index a382ae20ac7..d222e9cd3b3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.0.117-iimpi-2019.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13575/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['4e1fe2c705cfc47050064c0d6c4dee1a8c6740ac1c4f64dde9c7511c4989c7ad'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb index aa6a03a6929..ae7e676174e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb index e63cc1a2695..15e03750772 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb index 782473ec9fa..dcd07853ae8 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpi-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb index b8fb1ebef4c..af64b61bfd7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb index 3a5e6baedc4..e7a42454f04 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iompi-2019.01.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019.01'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14895/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb index 645ffaf31a7..8cd693cc5ec 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.02'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15095/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb index 2c06461ab97..8685b03cc91 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019.03'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15275/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb index 3c2759d1539..940151b46dc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb index 3421505968c..91ca97f6bc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-gompic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb index d95d740ea28..61489356fe3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb index 62cf27a5251..b1e88a55dd3 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iimpic-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb index 906ad9525cd..8e7d6fa5ec2 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.5.281-iompi-2019b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15816/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15816/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb index 610ba004009..d27b6e67346 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.0.166-iimpi-2020.00.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.00'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16232/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb index dcb4894a2a4..d662fdae171 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-gompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb index 89aac0e1547..a683875dd81 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020.06-impi-18.5.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020.06-impi-18.5'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb index 3111a3509b0..aef431b9b6d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb index 3475dab254a..dbfbc356455 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb index 3eca90fc0a2..1f80ac1e253 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iompi-2020a.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16533/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index 75ac380269e..71a9f0f37b9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'NVHPC', 'version': '21.2'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb index 541c3c12aea..1526523c788 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb index e07323d8ee3..570499af77d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb index e1f7dd0c3fd..15ccb6b8c77 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb index a350ab4a6ed..73aac3a85e7 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iimpic-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iimpic', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb index 89d0c991d88..68e2a157d3d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-iompi-2020b.eb @@ -11,7 +11,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'iompi', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16917/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb index 737f7462d7d..363e95f7dc9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.1.1-iimpi-2020.12.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2020.12'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17402/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17402/'] sources = ['l_onemkl_p_%(version)s.52_offline.sh'] checksums = ['818b6bd9a6c116f4578cda3151da0612ec9c3ce8b2c8a64730d625ce5b13cc0c'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb index ff7c13049ea..77a41fb58ed 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-gompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb index aa8f14f2250..741b626f55c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iimpi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb index 60282631f05..2bb82fd3380 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17757/'] sources = ['l_onemkl_p_%(version)s.296_offline.sh'] checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb index 07a876f213e..a4746816d23 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17901'] sources = ['l_onemkl_p_%(version)s.520_offline.sh'] checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb old mode 100755 new mode 100644 index a6e0651ef64..4f45be5badc --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'iompi', 'version': '2021b'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb index f3e3040b1ee..bacd9ba4607 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18222/'] sources = ['l_onemkl_p_%(version)s.640_offline.sh'] checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb index 67a5563ac0b..c348328e0e4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18444/'] sources = ['l_onemkl_p_%(version)s.117_offline.sh'] checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb index 2eb923c837e..955038d0fc1 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2022a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb index c34d533cf35..b0653443859 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18721/'] sources = ['l_onemkl_p_%(version)s.223_offline.sh'] checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb index 82776023871..a3c46807fc6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18898/'] sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb index 3daf55958a3..f2a7a15068e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19038/'] sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb index 4e6e5afb344..f29032bc3dd 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19138/'] sources = ['l_onemkl_p_%(version)s.25398_offline.sh'] checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb index 5e4f3cb8b1d..17ed1c0a2aa 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0-gompi-2023a.eb @@ -10,7 +10,7 @@ description = "Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2023a'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 21ad001e53c..a0341a987d6 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12405/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/12405/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['130b11571c3f71af00a722fa8641db5a1552ac343d770a8304216d8f5d00e75c'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb index e39879ac218..60f2eed4dd9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index f4e9e1a638f..0fc63f042f8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13063/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 060befc0a5a..75004db76a8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2018.5.274-GCC-7.3.0-2.30'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e6c3602e1e3..d4574181af9 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb index 137bf491a27..c28ff1e7e55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -6,7 +6,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13651/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb index 8f89b212fa4..4cb68a33fc8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2019.5.281.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb index 4c7b3a6b0df..e27d2ec5b55 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb index 02e2ace8251..2f959f48e46 100644 --- a/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2018.5.288-iccifortcuda-2019b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2019b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15614/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15614/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['3198257c19e82cd327d739b10120933e0547da8cddf8a8005677717326236796'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 2f60b422703..77755c77620 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.0.117-iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.0.117-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13584/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dfb403f49c1af61b337aa952b71289c7548c3a79c32c57865eab0ea0f0e1bc08'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8e2ed0b3980..6a222b3ed18 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.1.144-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14879/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/14879/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['dac86a5db6b86503313742b17535856a432955604f7103cb4549a9bfc256c3cd'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb index a5ba5409ff0..2bf8b19fb29 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.12.320-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17836/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17836/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['8108fbf2353a9f1926036bb67647b65c0e4933a3eb66e1dc933960e5b055f320'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 7cdc6aca429..5f75ad2ec68 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15040/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb index c0b1f565c0a..cb1ec1f179c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15260/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb index e19a15d6e33..49f0fa7a8d7 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.6.166-iccifort-2020.0.166-GCC-9.2.0.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.0.166-GCC-9.2.0'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16120/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb index d0ad0188c0d..07f8323810c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb index 557e0a8eab1..8a5646c25c1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020a'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/16546/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb index d4a9ef76ae4..d723d12dc1c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifort-2020.4.304.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb index 3305cf60a8d..7082d103ec8 100644 --- a/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb +++ b/easybuild/easyconfigs/i/impi/impi-2019.9.304-iccifortcuda-2020b.eb @@ -8,7 +8,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'iccifortcuda', 'version': '2020b'} -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17263/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17263/'] sources = ['l_mpi_%(version)s.tgz'] checksums = ['618a5dc2de54306645e6428c5eb7d267b54b11b5a83dfbcad7d0f9e0d90bb2e7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb index 1a0fbe3b035..d8a92d6db7e 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.1.1-intel-compilers-2021.1.2.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.1.2'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17397/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17397/'] sources = ['l_mpi_oneapi_p_%(version)s.76_offline.sh'] checksums = ['8b7693a156c6fc6269637bef586a8fd3ea6610cac2aae4e7f48c1fbb601625fe'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb index 345fd82fc3d..ecd3c9521f1 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17729/'] sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh'] checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index 8a736821926..1507acd5413 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17947'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb index a0c8a98edd8..24180258119 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18186/'] sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb index bee00810199..ea941c35ab2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18370/'] sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb index b1d328caa62..288c103cd03 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18714/'] sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh'] checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb index 8f400fabac4..2df8a69062f 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18926/'] sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb index 68aeb9beb63..aa2976fafaf 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19010/'] sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb index 86153bb28f5..89dce35e1f2 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb @@ -7,7 +7,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19131/'] sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh'] checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7'] diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..7404bfe1502 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.21.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.21.0' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.18' +local_commit = '124eec089e5d9ab5a2a2352461d03db6cdcf0ea0' +github_account = 'broadinstitute' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-15', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-34', { + 'checksums': ['d2047030e9f24c5dc8bbb378867fbcb8e71d1f1c2ab77e9285f79f670568f5f3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c8886c0a7c292e28a5fb0acaab3ae00eb2b3906aa0a1d146d5931819a37daefb'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb index 820a237e44d..67a5c1f5701 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.1.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17513/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17513/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.63_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17508/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17508/'], 'filename': 'l_fortran-compiler_p_%(version)s.62_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb index 4fe1af0da99..e4986d623f0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17749/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17756/'], 'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb index efcc5a7498b..cececeebef0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb @@ -12,11 +12,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17928/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17959/'], 'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb index b12d0b8bb3c..977bf5ced0e 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18209/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18210/'], 'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb index 56c8e9b5da4..967197cdfd7 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18435/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18436/'], 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb index b54023cfe84..011509935b0 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18478/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18481/'], 'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb index f25617230ac..92ac06db492 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18717/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18703/'], 'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb index 17262278b13..8c1390dae95 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18849/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18909/'], 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb index a6ae8170105..e67292301d5 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19030/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18998/'], 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb index 8d97d1ec3e5..f1e9b21f009 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb @@ -9,11 +9,11 @@ toolchain = SYSTEM # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html sources = [ { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19123/'], 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh', }, { - 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'], + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/19105/'], 'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh', }, ] diff --git a/easybuild/easyconfigs/i/intel/intel-2024.06.eb b/easybuild/easyconfigs/i/intel/intel-2024a.eb similarity index 97% rename from easybuild/easyconfigs/i/intel/intel-2024.06.eb rename to easybuild/easyconfigs/i/intel/intel-2024a.eb index 43a052dc1ea..7b08707e0fc 100644 --- a/easybuild/easyconfigs/i/intel/intel-2024.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2024a.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'intel' -version = '2024.06' +version = '2024a' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index 3deaaa9e711..ea2cfcb2650 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/17686/'] sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb index f9d10379c85..ea05e25db95 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18367/'] sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb index 22e6230e15b..0f35b870046 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb @@ -11,7 +11,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18694/'] sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh'] checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436'] diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..14ce45ca6ad --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.2.4' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['23a3d58cdeacf3abdf9fa1d81dcefee58da6ab330940790c0f27019703bfd2cd'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b1d3f620566 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..183e8e08ea4 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb new file mode 100644 index 00000000000..599edfd33ea --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.3-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.3-linux-x86_64.tar.gz': '81b910c922fff0e27ae1f256f2cc803db81f3960215281eddd2d484721928c70'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb new file mode 100644 index 00000000000..767a23c33a4 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.4-linux-x86_64.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.4' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +patches = [('julia.wrapper', 'bin/')] +checksums = [ + {'julia-1.10.4-linux-x86_64.tar.gz': '079f61757c3b5b40d2ade052b3cc4816f50f7ef6df668825772562b3746adff1'}, + {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'}, +] + +# install wrapper with linking safeguards for Julia libraries +postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"] + +sanity_check_paths = { + 'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share'] +} +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb index c193b35c83b..75355c6c842 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb @@ -1,6 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak # Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) # Updated by: Thomas Hoffmann (EMBL Heidelberg) easyblock = 'PythonBundle' @@ -8,7 +9,7 @@ name = 'jax' version = '0.4.25' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://pypi.python.org/pypi/jax' +homepage = 'https://jax.readthedocs.io/' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" @@ -18,8 +19,7 @@ cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9 builddependencies = [ ('Bazel', '6.3.1'), ('pytest-xdist', '3.3.1'), - # git 2.x required to fetch repository 'io_bazel_rules_docker' - ('git', '2.41.0', '-nodocs'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py ('poetry', '1.5.1'), ('pybind11', '2.11.1'), @@ -29,23 +29,65 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), ('NCCL', '2.18.3', versionsuffix), - ('zlib', '1.2.13'), ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('absl-py', '2.1.0'), ('flatbuffers-python', '23.5.26'), ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), ] # downloading xla and other tarballs to avoid that Bazel downloads it during the build -# note: this *must* be the exact same commit as used in third_party/{xla,"other"}/workspace.bzl +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' -local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' -local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" ' -local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' -local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' +components = [ + ('jaxlib', version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], + 'download_filename': '%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], + 'download_filename': '%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], + 'extract_cmd': local_extract_cmd, + }, + ], + 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], + 'checksums': [ + {'jaxlib-v0.4.25.tar.gz': + 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, + {'xla-4ccfe33c.tar.gz': + '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, + {'tf_runtime-0aeefb16.tar.gz': + 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, + {'jax-0.4.25_fix-pybind11-systemlib.patch': + 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'buildopts': _jaxlib_buildopts + }), +] # Some tests require an isolated run: local_isolated_tests = [ @@ -74,71 +116,20 @@ local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests]) use_pip = True -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, -} - -components = [ - ('absl-py', '2.1.0', { - 'options': {'modulename': 'absl'}, - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('jaxlib', version, { - 'sources': [ - '%(name)s-v%(version)s.tar.gz', - { - 'download_filename': '%s.tar.gz' % local_xla_commit, - 'filename': 'xla-%s.tar.gz' % local_xla_commit, - 'extract_cmd': local_extract_cmd, - }, - { - 'download_filename': '%s.tar.gz' % local_tfrt_commit, - 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit, - 'extract_cmd': local_extract_cmd, - }, - ], - 'source_urls': [ - 'https://github.com/google/jax/archive/', - 'https://github.com/tensorflow/runtime/archive', - 'https://github.com/openxla/xla/archive' - ], - 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], - 'checksums': [ - {'jaxlib-v0.4.25.tar.gz': - 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, - {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz': - '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, - {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz': - 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, - {'jax-0.4.25_fix-pybind11-systemlib.patch': - 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, - ], - 'start_dir': 'jax-jaxlib-v%(version)s', - # Avoid warning (treated as error) in upb/table.c - 'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"' - }), -] - exts_list = [ (name, version, { - 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], - 'runtest': local_test, 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], 'checksums': [ {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, {'jax-0.4.25_fix_env_test_no_log_spam.patch': 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, ], + 'runtest': local_test, }), ] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb similarity index 53% rename from easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb rename to easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb index 64a723ffe37..a4a86382ad6 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.4.25-foss-2023a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a.eb @@ -1,8 +1,8 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -# Updated by: Alex Domingo (Vrije Universiteit Brussel), Pavel Tománek (INUITS) -# Update v0.4.25 based on: https://github.com/easybuilders/easybuild-easyconfigs/pull/20119 - +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Updated by: Pavel Tománek (INUITS) +# Updated by: Thomas Hoffmann (EMBL Heidelberg) easyblock = 'PythonBundle' name = 'jax' @@ -12,14 +12,13 @@ homepage = 'https://jax.readthedocs.io/' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('Bazel', '6.3.1'), ('pytest-xdist', '3.3.1'), - # git 2.x required to fetch repository 'io_bazel_rules_docker' - ('git', '2.41.0', '-nodocs'), - ('matplotlib', '3.7.2'), + ('git', '2.41.0', '-nodocs'), # bazel uses git to fetch repositories + ('matplotlib', '3.7.2'), # required for tests/lobpcg_test.py ('poetry', '1.5.1'), ('pybind11', '2.11.1'), ] @@ -27,86 +26,84 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('zlib', '1.2.13'), + ('absl-py', '2.1.0'), ('flatbuffers-python', '23.5.26'), ('ml_dtypes', '0.3.2'), + ('zlib', '1.2.13'), ] -use_pip = True - +# downloading xla and other tarballs to avoid that Bazel downloads it during the build +local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives' +# note: following commits *must* be the exact same onces used upstream +# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4' +# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25' -local_extract_cmd = 'cp %s %(builddir)s/archives' - -local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" ' -local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' -local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' - -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, -} +# Use sources downloaded by EasyBuild +_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" ' +# Use dependencies from EasyBuild +_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" ' +_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" ' +# Avoid warning (treated as error) in upb/table.c +_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" ' components = [ - ('absl-py', '2.1.0', { - 'options': {'modulename': 'absl'}, - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), ('jaxlib', version, { 'sources': [ - '%(name)s-v%(version)s.tar.gz', { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/openxla/xla/archive'], 'download_filename': '%s.tar.gz' % local_xla_commit, - 'filename': 'xla-%s.tar.gz' % local_xla_commit, + 'filename': 'xla-%s.tar.gz' % local_xla_commit[:8], 'extract_cmd': local_extract_cmd, }, { + 'source_urls': ['https://github.com/tensorflow/runtime/archive'], 'download_filename': '%s.tar.gz' % local_tfrt_commit, - 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit, + 'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8], 'extract_cmd': local_extract_cmd, }, ], - 'source_urls': [ - 'https://github.com/google/jax/archive/', - 'https://github.com/tensorflow/runtime/archive', - 'https://github.com/openxla/xla/archive' - ], 'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'], 'checksums': [ {'jaxlib-v0.4.25.tar.gz': 'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'}, - {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz': + {'xla-4ccfe33c.tar.gz': '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'}, - {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz': + {'tf_runtime-0aeefb16.tar.gz': 'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'}, {'jax-0.4.25_fix-pybind11-systemlib.patch': 'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'}, ], 'start_dir': 'jax-jaxlib-v%(version)s', - # Avoid warning (treated as error) in upb/table.c - 'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"' + 'buildopts': _jaxlib_buildopts }), ] +use_pip = True + exts_list = [ (name, version, { + 'sources': [ + { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'filename': '%(name)s-v%(version)s.tar.gz', + }, + ], 'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'], - 'source_tmpl': '%(name)s-v%(version)s.tar.gz', - 'source_urls': ['https://github.com/google/jax/archive/'], 'checksums': [ {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'}, {'jax-0.4.25_fix_env_test_no_log_spam.patch': 'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'}, ], + 'runtest': "pytest -n %(parallel)s tests", }), ] sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..023c3001dd3 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb new file mode 100644 index 00000000000..db6e77ea520 --- /dev/null +++ b/easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb @@ -0,0 +1,28 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'joypy' +version = '0.2.6' + +homepage = 'https://github.com/sbebo/joypy' +description = "Joyplots in Python with matplotlib & pandas" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_WHL] +checksums = ['fffe882e8281e56e08b374a3148436cb448562ba39e4d566204c7e8ee2caddab'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..87642888aa1 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.17' +local_suff = '-20230812' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..03dceec3b87 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-9.0.2-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '9.0.2' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a599a77e406e59cdb7672d780e69156b6ce57cb8ce515d21d1744c4065a85976'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ceaec648de3 --- /dev/null +++ b/easybuild/easyconfigs/j/junos-eznc/junos-eznc-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'junos-eznc' +version = '2.7.1' + +homepage = 'https://github.com/Juniper/py-junos-eznc' +description = "Python library for Junos automation." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('PyYAML', '6.0'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +exts_list = [ + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('transitions', '0.9.2', { + 'checksums': ['2f8490dbdbd419366cef1516032ab06d07ccb5839ef54905e842a472692d4204'], + }), + ('scp', '0.15.0', { + 'checksums': ['f1b22e9932123ccf17eebf19e0953c6e9148f589f93d91b872941a696305c83f'], + }), + ('pyserial', '3.5', { + 'modulename': 'serial', + 'checksums': ['3c77e014170dfffbd816e6ffc205e9842efb10be9f58ec16d3e8675b4925cddb'], + }), + ('ncclient', '0.6.15', { + 'checksums': ['6757cb41bc9160dfe47f22f5de8cf2f1adf22f27463fb50453cc415ab96773d8'], + }), + ('paramiko', '3.4.0', { + # Juniper fork of paramiko - compatible with junos-eznc + 'source_urls': ['https://github.com/Juniper/paramiko/archive/'], + 'sources': [{'download_filename': 'v%(version)s-JNPR.tar.gz', 'filename': '%(name)s-%(version)s-JNPR.tar.gz'}], + 'checksums': ['6b3b62e18a2b693169eaa50a7cdd2ab5637fc423205ce85e109cb37722f9eeda'], + }), + (name, version, { + 'modulename': 'jnpr.junos', + # delete 'os.system("pip install git+https://github.com/Juniper/paramiko.git@v3.4.0-JNPR")' from setup.py + 'preinstallopts': "sed -i '/pip install/d' setup.py && ", + 'checksums': ['371f0298bf03e0cb4c017c43f6f4122263584eda0d690d0112e93f13daae41ac'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..231466bb169 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +if ARCH == 'x86_64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl' +elif ARCH == 'aarch64': + local_source_tmpl = '%(namelower)s-%(version)s-py2.py3-none-manylinux2014_%(arch)s.whl' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'checksums': ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb new file mode 100644 index 00000000000..e4fd527e908 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-468-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '468' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8'] + +dependencies = [ + ('MariaDB', '11.6.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('util-linux', '2.39'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.13.0'), +] + +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4dd6b4afdf1 --- /dev/null +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'kineto' +version = '0.4.0' + +homepage = 'https://github.com/pytorch/kineto' +description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pytorch/kineto/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +start_dir = 'libkineto' + +sanity_check_paths = { + 'files': ['lib/libkineto.a'], + 'dirs': ['include/kineto'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1fa3ca78fd9 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [('ncurses', '6.5')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +preconfigopts += "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f0d3a361152 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.39.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.39.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['839bac36f6073318e36f0b163767e03bdbd3f57d99256b97494ac439b59a4562'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '16.0.6'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..946dd8e0961 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a10be56a891 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.42')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb new file mode 100644 index 00000000000..143e59d35c5 --- /dev/null +++ b/easybuild/easyconfigs/l/LRBinner/LRBinner-0.1-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'LRBinner' +version = '0.1' + +homepage = 'https://github.com/anuradhawick/LRBinner' +description = "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB. " + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HMMER', '3.4'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('Biopython', '1.83'), + ('scikit-learn', '1.3.1'), + ('FragGeneScan', '1.31'), + ('HDBSCAN', '0.8.38.post1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tabulate', '0.9.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f'], + }), + (name, version, { + 'modulename': 'mbcclr_utils', + 'preinstallopts': "sed -i 's/pytorch/torch/g' setup.py && ", + 'source_urls': ['https://github.com/anuradhawick/LRBinner/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['2d77dde8ab1272c432b20eb18a352326c622e929261562ef6d680c6638cc4bd1'], + }), +] + +sanity_check_commands = ['LRBinner --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4d8ccd20b1f --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee92fb98c62 --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.84.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.84.1' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b3e1254b1cca381e77c819b59ca99774ff43530209b9aeb511e1d46588a64f6'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.1'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..121d33200a2 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.16' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['d873d34ad8b9b4cea010631f1a6228d2087475e4dc5e763eb81acc23d9d45a51'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('libjpeg-turbo', '3.0.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8a01a3ac439 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('Ninja', '1.12.1'), + ('Meson', '1.4.0'), +] + +dependencies = [('Mesa', '24.1.3')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb new file mode 100644 index 00000000000..1ea2630b327 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2024a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb index 237260a43f7..063ce985f47 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.38'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.38'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb index 39e628f1d97..a6dbd52797f 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-12.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['319e9771d037b6c796f04e6a96bb27db1706bc5931ca149c78347c623a747771'] builddependencies = [ ('binutils', '2.40'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('Autotools', '20220317'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.39'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb index e2bb8f718ab..c1cb33551f7 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6e907ea7a9f878965a3af2a858423450dde389d851fc67a33b0096b8b9b6085'] builddependencies = [ ('binutils', '2.36.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210128'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.36'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb index b48c3f1b6bc..1172b66d8f2 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -9,14 +9,15 @@ description = """A C++ SDK which contains an implementation of DAP 2.0 and toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://www.opendap.org/pub/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb'] +source_urls = ['https://github.com/OPENDAP/libdap4/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e59b48f48bb37b36dcf9618043881e1d4150abd9b2ea3fa7474647c4ad622ccc'] builddependencies = [ ('binutils', '2.37'), ('Bison', '3.7.6'), ('flex', '2.6.4'), + ('Autotools', '20210726'), ] dependencies = [ @@ -27,6 +28,7 @@ dependencies = [ ('util-linux', '2.37'), ] +preconfigopts = "autoreconf -fi && " configopts = 'TIRPC_LIBS="-ltirpc"' sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..95a46c43114 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.10.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.10.1' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['b511a2dc78b98786064889deaa2c1bc48a0c70115c187900dd838474ded1cc19'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('elfutils', '0.191'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..098fd8b7bde --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20240517-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20240517' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['3a489097bb4115495f3bd85ae782852b7097c556d9500088d74b6fa38dbd12ff'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..07da30e2a80 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.8.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c1eaf0cf07cba0e9021920bfba9502140220786ed5d8a8ec6c7ad9174522f8e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('PCRE2', '10.43'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '-DREGEX_BACKEND=pcre2' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch new file mode 100644 index 00000000000..3f592cadb0d --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/003-guile2.0.patch @@ -0,0 +1,402 @@ +Description: Increase precision of floating point tests + guile-2.0 has increased the precision of the floating point maths returns, + so the test suite needs to allow for the correct values to be returned + with higher precision. Thanks to Dave Pigott + Also adapt the configure script to build against guile-2.0 - patch from + Hilo Bengen . + . + libmatheval (1.1.11+dfsg-1.1) unstable; urgency=low + . + * Non-maintainer upload. + * Migrate to guile-2.0 - patch from Hilo Bengen, + extended to support higher precision of return values + by guile-2.0. (Closes: #746013) +Author: Neil Williams +Bug-Debian: https://bugs.debian.org/746013 + +--- + +--- libmatheval-1.1.11+dfsg.orig/configure.in ++++ libmatheval-1.1.11+dfsg/configure.in +@@ -60,10 +60,11 @@ dnl Checks for library functions. + AC_CHECK_FUNCS([bzero memset], [break]) + + dnl Additional Guile feature checks. ++CFLAGS="$CFLAGS $GUILE_CFLAGS" + AC_CHECK_TYPE([scm_t_bits], [AC_DEFINE([HAVE_SCM_T_BITS], [1], [Define to 1 if you have the `scm_t_bits' type.])], [], [#include ]) +-AC_CHECK_LIB([guile], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) +-AC_CHECK_LIB([guile], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_c_define_gsubr], [AC_DEFINE([HAVE_SCM_C_DEFINE_GSUBR], [1], [Define to 1 if you have the `scm_c_define_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_make_gsubr], [AC_DEFINE([HAVE_SCM_MAKE_GSUBR], [1], [Define to 1 if you have the `scm_make_gsubr' function.])], [], [$GUILE_LDFLAGS]) ++AC_CHECK_LIB([guile-2.0], [scm_num2dbl], [AC_DEFINE([HAVE_SCM_NUM2DBL], [1], [Define to 1 if you have the `scm_num2dbl' function.])], [], [$GUILE_LDFLAGS]) + + AC_CONFIG_FILES([Makefile doc/Makefile lib/Makefile]) + AC_OUTPUT(libmatheval.pc) +--- libmatheval-1.1.11+dfsg.orig/tests/basics.at ++++ libmatheval-1.1.11+dfsg/tests/basics.at +@@ -62,7 +62,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -70,7 +70,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x f 0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [0.220966666722528], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [0.22096666672252796], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -78,7 +78,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y f 0.4 -0.7)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [-1.14962406520749], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [-1.1496240652074883], [ignore]) + + AT_DATA([basics.scm], + [[ +@@ -86,7 +86,7 @@ AT_DATA([basics.scm], + (display (evaluator-evaluate-x-y-z f 11.2 0.41 -0.66)) + ]]) + +-AT_CHECK([matheval.sh basics.scm], [ignore], [3.99876152571934], [ignore]) ++AT_CHECK([matheval.sh basics.scm], [ignore], [3.9987615257193383], [ignore]) + + AT_DATA([basics.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/constants.at ++++ libmatheval-1.1.11+dfsg/tests/constants.at +@@ -29,7 +29,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -37,7 +37,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.44269504088896], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4426950408889634], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -45,7 +45,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.434294481903252], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.4342944819032518], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -53,7 +53,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.693147180559945], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6931471805599453], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -61,7 +61,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [2.30258509299405], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [2.302585092994046], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -69,7 +69,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [3.14159265358979], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [3.141592653589793], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -77,7 +77,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -85,7 +85,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -93,7 +93,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.318309886183791], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.3183098861837907], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -101,7 +101,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.636619772367581], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.6366197723675814], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -109,7 +109,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.12837916709551], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.1283791670955126], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -117,7 +117,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623731], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [1.4142135623730951], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -125,7 +125,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [0.707106781186548], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [0.7071067811865476], [ignore]) + + AT_DATA([constant.scm], + [[ +@@ -133,7 +133,7 @@ AT_DATA([constant.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh constant.scm], [ignore], [10.0], [ignore]) ++AT_CHECK([matheval.sh constant.scm], [ignore], [10.000000000000002], [ignore]) + + AT_DATA([constant.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/functions.at ++++ libmatheval-1.1.11+dfsg/tests/functions.at +@@ -29,7 +29,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [2.71828182845905], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [2.718281828459045], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -80,7 +80,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.841470984807897], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8414709848078965], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -97,7 +97,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.54030230586814], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5403023058681398], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -114,7 +114,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5574077246549023], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -131,7 +131,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.642092615934331], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6420926159343306], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -148,7 +148,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.85081571768093], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.8508157176809255], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -165,7 +165,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.18839510577812], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1883951057781212], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -182,7 +182,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -216,7 +216,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -233,7 +233,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.785398163397448], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7853981633974483], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -267,7 +267,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267949], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5707963267948966], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -284,7 +284,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.1752011936438014], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -301,7 +301,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.54308063481524], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.5430806348152437], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -318,7 +318,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.761594155955765], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.7615941559557649], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -335,7 +335,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [1.31303528549933], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [1.3130352854993315], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -352,7 +352,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.648054273663885], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.6480542736638855], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -368,7 +368,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.850918128239322], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8509181282393216], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -385,7 +385,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -419,7 +419,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 0.5)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -436,7 +436,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 2)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.549306144334055], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.5493061443340549], [ignore]) + + AT_DATA([function.scm], + [[ +@@ -470,7 +470,7 @@ AT_DATA([function.scm], + (display (evaluator-evaluate-x f 1)) + ]]) + +-AT_CHECK([matheval.sh function.scm], [ignore], [0.881373587019543], [ignore]) ++AT_CHECK([matheval.sh function.scm], [ignore], [0.8813735870195429], [ignore]) + + AT_DATA([function.scm], + [[ +--- libmatheval-1.1.11+dfsg.orig/tests/numbers.at ++++ libmatheval-1.1.11+dfsg/tests/numbers.at +@@ -53,6 +53,6 @@ AT_DATA([number.scm], + (display (evaluator-evaluate-x f 0)) + ]]) + +-AT_CHECK([matheval.sh number.scm], [ignore], [0.644394014977254], [ignore]) ++AT_CHECK([matheval.sh number.scm], [ignore], [0.6443940149772542], [ignore]) + + AT_CLEANUP diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b8bf07966b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' # still the latest version available on the ftp mirror + +homepage = 'https://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '003-guile2.0.patch', + 'libmatheval-1.1.11_fix-matheval-test.patch' +] +checksums = [ + {'libmatheval-1.1.11.tar.gz': '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab'}, + {'003-guile2.0.patch': 'd0ad39d54800153cbaa26c01448f040d405f09e9fd57e1357eab170a274a9b5c'}, + {'libmatheval-1.1.11_fix-matheval-test.patch': '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('byacc', '2.0.20240109'), + # guile 2.2.X, 3.0.7 removed scm_num2dbl (among others), which are needed for libmatheval (at least for 1.1.11) + ('Guile', '2.0.14') +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb new file mode 100644 index 00000000000..e0e689460f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ELSI', '2.9.1', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb new file mode 100644 index 00000000000..260ecb98ddb --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.12.6-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.12.6' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'libmbd' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9f8154b6b2f57e78a8e33d3b315a244185e8e5ecb03661a469808af7512e761e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ELSI', '2.11.0', '-PEXSI'), +] + +# build scripts expect either a git repo or a defined version string in a file +_versiontag_file = '%(builddir)s/%(name)s-%(version)s/cmake/LibmbdVersionTag.cmake' +preconfigopts = "echo 'set(VERSION_TAG \"%%(version)s\")' > %s && " % _versiontag_file + +configopts = "-DENABLE_SCALAPACK_MPI=ON -DENABLE_ELSI=ON " +configopts += "-DMPIEXEC_MAX_NUMPROCS=1 " # number of procs in the tests + +# make sure that built libraries (libmbd.so) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd/mbd.h', 'include/mbd/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..818f1687a15 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libtirpc', '1.3.5'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..810ddbe1169 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.42')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..c09615c86f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.5.2' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65c1d2f78b9f2fb20082c38cbe47c951ad5839345876e46941612ee87f9a7ce1'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb index 444e2ba800d..c26fed6c2e3 100644 --- a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb +++ b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb @@ -27,7 +27,6 @@ use_pip = True exts_list = [ ('soxr', '0.3.7', { - 'preinstallopts': 'python -m build && ', 'checksums': ['436ddff00c6eb2c75b79c19cfdca7527b1e31b5fad738652f044045ba6258593'], }), ('audioread', '3.0.1', { diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e60ad09d1a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-13.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('FLAC', '1.4.3'), + ('libvorbis', '1.3.7'), + ('libopus', '1.5.2'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e98d28304a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.20-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.20' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['ebb65ef6ca439333c2bb41a0c1990587288da07f6c7fd07cb3a18cc18d30ce19'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1752b337b05 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-2.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '2.0.0' + +homepage = 'https://libspatialindex.org' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['f1d5a369681fa6ac3301a54db412ccf3180fc17163ebc3252f32c752f77345de'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a9fc2a5d749 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.5' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['9b31370e5a38d3391bf37edfa22498e28fe2142467ae6be7a17c9068ec0bf12f'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7fa2f46eb1f --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.2-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.2' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['632bd65ed74a881ca8a0309a1001c428bd1cbd5cd7ddbf8cedcd2e65f4dcdc44'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7e32c5c3a99 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..70084689c61 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.4.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61f873ec69e3be1b99535634340d5bde750b2e4447caa1db9f61be3fd49ab1e5'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a38c53ef841 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.42-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.42' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['85ca62cac0d41fc77d3f6033da9df6fd73d20ea2fc18b0a3609ffb4110e1baeb'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('libxml2', '2.12.7'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..ce954f2edae --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('cutadapt', '4.9'), + ('BCFtools', '1.18'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.1'), + ('gawk', '5.3.0'), + ('medaka', '1.11.3'), + ('minimap2', '2.26'), + ('parallel', '20230722'), + ('Pysam', '0.22.0'), + ('Racon', '1.5.0'), + ('SAMtools', '1.18'), + ('seqtk', '1.4'), + ('VSEARCH', '2.25.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version +local_deps_patch = ( + "sed -i " + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb new file mode 100644 index 00000000000..7681d5bf0a9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa14572bef6 --- /dev/null +++ b/easybuild/easyconfigs/l/lrcalc/lrcalc-2.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'lrcalc' +version = '2.1' + +homepage = 'https://sites.math.rutgers.edu/~asbuch/lrcalc/' +description = """The Littlewood-Richardson Calculator is a program + designed to compute Littlewood-Richardson coefficients.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://math.rutgers.edu/~asbuch/lrcalc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['996ac00e6ea8321ef09b34478f5379f613933c3254aeba624b6419b8afa5df57'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': [ + 'bin/lrcalc', + 'lib/liblrcalc.%s' % SHLIB_EXT, + 'include/lrcalc/ivector.h', + ], + 'dirs': [] +} + +sanity_check_commands = ["lrcalc 2>&1 | grep '^Usage:'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb new file mode 100644 index 00000000000..c36ee58b273 --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.6-gompi-2024a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.6' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['108e622441028b7f88223244c9117d5de18a91fd7c246bfa48802b5c585557d0'] + +builddependencies = [ + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..0af2dcbed3f --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-5.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '5.3.0' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('libxml2', '2.12.7'), + ('libxslt', '1.1.42'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..c5c3ad83f3a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-14.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..dbba96ddf2f --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2', versionsuffix), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb new file mode 100644 index 00000000000..e7e73a89e80 --- /dev/null +++ b/easybuild/easyconfigs/m/MATES/MATES-0.1.2-20240813-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'MATES' +version = '0.1.2-20240813' +local_commit = 'd5ee15b' + +homepage = 'https://github.com/mcgilldinglab/MATES' +description = "A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('SAMtools', '1.18'), + ('pybedtools', '0.9.1'), + ('PyTorch-bundle', '2.1.2'), + ('Pysam', '0.22.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + (name, version, { + 'modulename': 'MATES', + # unpin exact versions of dependencies + 'preinstallopts': r"sed -i 's/==.*//g' requirements.txt && sed -i 's/==.*/\",/g' setup.py && ", + 'source_urls': ['https://github.com/mcgilldinglab/MATES/archive'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['aca36b2b99ebed975fdf61670a9b551c1ab7882ff2b9d4ed3f25f2e13805652c'], + }), +] + +sanity_check_commands = [ + "python -c 'from MATES import bam_processor, data_processor, MATES_model'", + "python -c 'from MATES import TE_quantifier, TE_quantifier_LongRead, TE_quantifier_Intronic'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..3f6da986d62 --- /dev/null +++ b/easybuild/easyconfigs/m/MBX/MBX-1.1.0-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MBX' +version = '1.1.0' + +homepage = 'https://github.com/paesanilab/MBX' +description = "MBX is an energy and force calculator for data-driven many-body simulations" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/paesanilab/MBX/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['0f55f4950226defb46fd0814ad97f906ce4ffd6403af6817bd98cb3c68996692'] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GSL', '2.7'), +] + +preconfigopts = 'export MBX_HOME=$PWD && autoreconf -fi && ' + +configopts = '--enable-shared --enable-verbose CXX="$CXX"' + +postinstallcmds = ["cp -a plugins %(installdir)s"] + +maxparallel = 2 + +runtest = 'check' + +modextrapaths = {'PYTHONPATH': 'plugins/python'} + +modextravars = {'MBX_HOME': '%(installdir)s'} + +sanity_check_paths = { + 'files': ['bin/mb_decomp', 'bin/optimize', 'bin/order_frames', 'bin/single_point', + 'lib/libmbx.a', 'lib/libmbx.%s' % SHLIB_EXT], + 'dirs': ['include', 'plugins/python/mbx', 'plugins/lammps/USER-MBX'], +} + +sanity_check_commands = [ + "optimize", + "python -c 'import mbx'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb new file mode 100644 index 00000000000..43dcfb25294 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022b.10.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2022b' # runtime version 9.13 +local_update = '10' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['5bcee3f2be7a4ccb6ed0b7d8938eca7b33e4a0d81ec5351d6eb06150a89245eb'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb new file mode 100644 index 00000000000..b6832290ecb --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2023b.9.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2023b' # runtime version 23.2 +local_update = '9' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['ef69a624806aa3864d692a88a67d969e3b641ae296b4a091969185ef056f13bd'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..417e4750ef9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb new file mode 100644 index 00000000000..5b4aedbdadb --- /dev/null +++ b/easybuild/easyconfigs/m/MOKIT/MOKIT-1.2.6_20240830-gfbf-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'MOKIT' +version = '1.2.6_20240830' +_commit = 'd66560a6a7926e5e21b45cbcc9213aaa26bd997d' + +homepage = 'https://github.com/1234zou/MOKIT' +description = """ +MOKIT offers various utilities and modules to transfer MOs among various quantum chemistry software packages.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +_makefile = 'Makefile.gnu_openblas_conda' +maxparallel = 1 + +default_component_specs = { + 'source_urls': ['https://github.com/1234zou/MOKIT/archive'], + 'checksums': ['b4e7224ac5b56e6d0116f7759a3017c57d527b1d35c32e3b2733904f7f7c4de5'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + }], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'MOKIT-%s/src' % _commit, + 'prebuildopts': 'sed -i -e "s/^MKL_FLAGS.*/MKL_FLAGS = $LIBBLAS/" %s && ' % _makefile, + 'buildopts': 'all -f %s' % _makefile, + 'files_to_copy': ['../bin'], + }), + ('mokit', version, { + 'easyblock': 'PythonPackage', + 'start_dir': 'MOKIT-%s' % _commit, + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'mokit'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'fch2inp | grep Example', + 'geom_opt | grep Example', + "python -s -c 'from mokit.lib.gaussian import load_mol_from_fch'", +] + +sanity_check_paths = { + 'files': ['bin/geom_opt', 'bin/fch2inp'], + 'dirs': ['lib/python3.11/site-packages/mokit'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb new file mode 100644 index 00000000000..29dbbe424ba --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'Project-MONAI' + +builddependencies = [ + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyTorch', '1.13.1'), + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.21.0'), + ('tensorboard', '2.15.1'), + ('torchvision', '0.14.1'), + ('tqdm', '4.64.1'), + ('Pillow', '9.4.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.11.1'), +] + +use_pip = True + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel," +local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy," +local_pip_extras += "skimage,tensorboard,torchvision,tqdm" + +# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'}, + ], + }), + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'use_pip_extras': local_pip_extras, + # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point + # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617 + 'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2', + '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')], + }), +] + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +local_extra_mod_check = {x: x for x in local_pip_extras.split(",")} +# Some special cases with different module name than extra name +local_extra_mod_check['pillow'] = 'PIL' +local_extra_mod_check['pyyaml'] = 'yaml' + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb new file mode 100644 index 00000000000..2b2b2185ecc --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-4.2.2-GCC-13.3.0.eb @@ -0,0 +1,21 @@ +name = 'MPICH' +version = '4.2.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://www.mpich.org/static/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41'] + +dependencies = [ + ('UCX', '1.16.0'), +] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..35743343440 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-11.6.0-GCC-12.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '11.6.0' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-11.6.0.tar.gz': '8fd5b593aee3920eb434c37ec44779d565fe96ef7dfd6b35a646fe7221103e11'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.4.2'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.10'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.11.4'), # needed by Connect XML + ('Boost', '1.82.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.42'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..04b5629d6bf --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.7-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.7' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a733004f29a --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.8.1-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'Mercurial' +version = '6.8.1' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.%(namelower)s-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['030e8a7a6d590e4eaeb403ee25675615cd80d236f3ab8a0b56dcc84181158b05'] + +dependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ['hg --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..a757e81653a --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.1' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [('Boost', '1.85.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..65102800699 --- /dev/null +++ b/easybuild/easyconfigs/m/mallard-ducktype/mallard-ducktype-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mallard-ducktype' +version = '1.0.2' + +homepage = 'https://github.com/projectmallard/mallard-ducktype' +description = """Parser for the lightweight Ducktype syntax for Mallard""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['mallard_ducktype-%(version)s-py3-none-any.whl'] +checksums = ['90c2d9e40934c634f3e83e0758285e2803f62c2c5db405702af2f5884e1a2918'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +options = {'modulename': 'mallard.ducktype'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb index 4587e8e91df..ff224b45ba2 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-GCC-10.2.0-Python-2.7.18.eb @@ -62,9 +62,7 @@ sanity_check_paths = { 'dirs': ['libexec'], } -sanity_check_commands = [ - 'python %(installdir)s/bin/runMantaWorkflowDemo.py' -] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb index 8e5943d0213..2d6c80a9b71 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb index 0b2b3af8477..7633e9131e0 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.6.0-gompi-2020a-Python-2.7.18.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': ['lib/python', 'share'], } -sanity_check_commands = ['runMantaWorkflowDemo.py'] +sanity_check_commands = ['cd "$(mktemp -d)" && runMantaWorkflowDemo.py'] modextrapaths = { 'PATH': 'libexec', diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch new file mode 100644 index 00000000000..9a34eb1cdae --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-contourpy-fix-pybind-module.patch @@ -0,0 +1,14 @@ +Fixes: error: macro "PYBIND11_MODULE" passed 3 arguments, but takes just 2 +Author: Anke Kreuzer (JSC) +diff -ruN src/wrap.cpp.orig src/wrap.cpp +--- src/wrap.cpp.orig 2024-09-02 21:07:13.893013182 +0200 ++++ src/wrap.cpp 2024-09-02 21:07:39.973005828 +0200 +@@ -18,7 +18,7 @@ + static contourpy::LineType mpl20xx_line_type = contourpy::LineType::SeparateCode; + static contourpy::FillType mpl20xx_fill_type = contourpy::FillType::OuterCode; + +-PYBIND11_MODULE(_contourpy, m, py::mod_gil_not_used()) { ++PYBIND11_MODULE(_contourpy, m) { + m.doc() = + "C++11 extension module wrapped using `pybind11`_.\n\n" + "It should not be necessary to access classes and functions in this extension module " diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb new file mode 100644 index 00000000000..33ddf00eb93 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.9.2-gfbf-2024a.eb @@ -0,0 +1,79 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.9.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('cppy', '1.2.1'), + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('libpng', '1.6.43'), + ('freetype', '2.13.2'), + ('Tkinter', '%(pyver)s'), + ('Pillow-SIMD', '10.4.0'), + ('Qhull', '2020.2'), +] + +use_pip = True +sanity_pip_check = True + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_configopts = "--config-settings=setup-args='-Dsystem-qhull=true' && " +local_configopts += " --config-settings=setup-args='-Dsystem-freetype=true' && " +local_configopts += "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('Cycler', '0.12.1', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'], + }), + ('kiwisolver', '1.4.5', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.3.0', { + 'patches': ['matplotlib-3.9.2-contourpy-fix-pybind-module.patch'], + 'checksums': [ + {'contourpy-1.3.0.tar.gz': '7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4'}, + {'matplotlib-3.9.2-contourpy-fix-pybind-module.patch': + 'a998438a1048524a550bf3bb607197658b13dce56e8e54169e24ce7c3c022a8f'}, + ], + }), + (name, version, { + 'configopts': "%(local_configopts)s", + 'checksums': ['96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..87f92553548 --- /dev/null +++ b/easybuild/easyconfigs/m/mcqd/mcqd-1.0.0-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CmdCp' + +name = 'mcqd' +version = '1.0.0' + +homepage = 'https://gitlab.com/janezkonc/mcqd' +description = """MaxCliqueDyn is a fast exact algorithm for finding a maximum clique in an undirected graph.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/janezkonc/mcqd/-/archive/v%(version)s/'] +sources = ['mcqd-v%(version)s.tar.gz'] +checksums = ['37ff68ff88e047c929990d4c12ce474753f6f9c49324661a3aa1cfe77c26ad9d'] + +cmds_map = [('.*', '$CXX $CXXFLAGS $LDFLAGS mcqd.cpp -o mcqd')] + +files_to_copy = [ + (['mcqd'], 'bin'), + (['mcqd.h'], 'include'), +] + +sanity_check_paths = { + 'files': [ + 'bin/mcqd', + 'include/mcqd.h', + ], + 'dirs': [], +} + +sanity_check_commands = ["command -v mcqd"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..e8ec2b8435d --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('json-fortran', '9.0.2'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c9ac4870bf5 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,85 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.1', { + 'checksums': ['878f981e890a421d92a0d7606705d0ad9813ae6086239460dfe4b0cfc7476174'], + }), + (name, version, { + 'checksums': ['039219204111a8114b1f72d87d0d3463e43473790cff4520c8afbd79cc8784d6'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3e055e5d8dd --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,88 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.15.1', versionsuffix), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb new file mode 100644 index 00000000000..f95d01c89d9 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.12.1-foss-2023a.eb @@ -0,0 +1,86 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.12.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.2'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", + # ont-parasail on PyPI is just pre-built wheels for (python-)parasail + "sed -i 's/ont-parasail/parasail/g' requirements.txt", +] + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0b2749c2cde3ef640bf314a9f94b24d929fe1ca476974719a6909dfc568c3aac'], + }), + # medaka 1.12.0 requires h5py ~=3.10.0 + ('h5py', '3.10.0', { + 'checksums': ['d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049'], + }), + ('pyabpoa', '1.5.2', { + 'checksums': ['be39c83b12e923c9e47073cb8f0abc4c42f609fa2c0ec13d6f6a4f5a0537ee06'], + }), + (name, version, { + 'checksums': ['df4baf7d1e9154de85229aef237919619ff6ae7f7d103abb0828e449ff977adf'], + # Some requirements are too strict. + 'preinstallopts': " && ".join(local_sed_commands) + " && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..94f332d290b --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.28-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +# Update Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.28' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['ffa5712735d229119f8c05722a0638ae0cc15aeb8938e29a3e52d5da5c92a0b4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aa598c6869b --- /dev/null +++ b/easybuild/easyconfigs/m/miniprot/miniprot-0.13-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = "MakeCp" + +name = 'miniprot' +version = '0.13' + +homepage = 'https://github.com/lh3/miniprot' +description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. +It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. +Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much +faster at the residue alignment step.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/miniprot/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('zlib', '1.2.13')] + +files_to_copy = [ + (['*.h', 'miniprot.1', 'test', 'tex'], 'lib'), + (['miniprot'], 'bin'), + 'README.md', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/miniprot'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb new file mode 100644 index 00000000000..f486ed4effd --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('attr', '2.5.2'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.6'), + ('dtcmp', '1.1.5'), + ('libarchive', '3.7.4'), + ('libcircle', '0.3'), +] + +_binaries = [ + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind', + 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..a609b4e373b --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.3.0-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['56b3d778629eb74b8a515cd53c727d04609f858a07f8d3555fd5fd392a206dcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb new file mode 100644 index 00000000000..b4ccfa2544f --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gfbf-2023a.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb new file mode 100644 index 00000000000..2bac0d9bfe6 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.15' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'] + +dependencies = [ + ('Python', '3.10.8'), + ('dill', '0.3.7'), + ('Arrow', '11.0.0'), # if needed rebuild --from-pr 19758 +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index c85b7a97e48..569d09f9859 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,11 +11,15 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.16.2_fix-cpuid.patch'] +patches = [ + 'NCCL-2.16.2_fix-cpuid.patch', + 'NCCL-2.18.3_fix-cudaMemcpyAsync.patch', +] checksums = [ ('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'), {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, + {'NCCL-2.18.3_fix-cudaMemcpyAsync.patch': '7dc8d0d1b78e4f8acefbc400860f47432ef67c225b50d73c732999c23483de90'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch new file mode 100644 index 00000000000..68542656733 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3_fix-cudaMemcpyAsync.patch @@ -0,0 +1,174 @@ +Backported from (original message attached below): +https://github.com/NVIDIA/nccl/commit/4365458757e4107ecbf629b2fd6e0e19a5d237c2 + +From: Kaiming Ouyang +Date: Wed, 20 Sep 2023 05:51:14 -0700 +Subject: [PATCH] Fix cudaMemcpyAsync bug + +We are trying to use the copy result of first cudaMemcpyAsync in the +second cudaMemcpyAsync without sync in between. This patch fixes it +by allocating a CPU side array to cache device side addr so that we +can avoid this consecutive cuda mem copy. + +Fixes #957 +--- + src/channel.cc | 12 ++++++++++++ + src/include/comm.h | 2 ++ + src/init.cc | 2 +- + src/transport.cc | 8 ++------ + src/transport/nvls.cc | 10 ++++------ + 5 files changed, 21 insertions(+), 13 deletions(-) + +diff --git a/src/channel.cc b/src/channel.cc +index 3edcc2f..245dfd5 100644 +--- a/src/channel.cc ++++ b/src/channel.cc +@@ -42,9 +42,11 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + /* channel->devPeers is not shared, so just free it when calling commFree() */ + NCCLCHECK(ncclCudaCallocAsync(&channel->devPeers, nPeers, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devPeers); ++ NCCLCHECK(ncclCalloc(&channel->devPeersHostPtr, nPeers)); + for (int r = 0; r < nRanks; r++) { + uintptr_t addr = (uintptr_t)(comm->sharedRes->devPeers[channelId] + comm->topParentRanks[r]); + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[r] = (struct ncclDevChannelPeer*)addr; + } + } + +@@ -52,6 +54,8 @@ ncclResult_t initChannel(struct ncclComm* comm, int channelId) { + NCCLCHECK(ncclCudaCallocAsync(&channel->devRingUserRanks, nRanks, sharedRes->deviceStream.cudaStream)); + ncclCommPushCudaFree(comm, channel->devRingUserRanks); + ++ /* guarantee addr has been copied into channel->devPeers */ ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -77,6 +81,7 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(parent->channels[channelId].nvlsDevPeers + tr); + channel->peers[comm->nRanks + 1 + r] = parent->channels[channelId].nvlsPeers + tr; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].nvlsPeers[tr].refCount); + } + } else { +@@ -86,10 +91,12 @@ ncclResult_t initNvlsChannel(struct ncclComm* comm, int channelId, struct ncclCo + uintptr_t addr = (uintptr_t)(channel->nvlsDevPeers + r); + channel->peers[comm->nRanks + 1 + r] = channel->nvlsPeers + r; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks + 1 + r), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks + 1 + r] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->nvlsPeers[r].refCount); + } + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -114,6 +121,7 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)parent->channels[channelId].collnetDevPeers; + channel->peers[comm->nRanks] = parent->channels[channelId].collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&parent->channels[channelId].collnetPeers->refCount); + } else { + NCCLCHECK(ncclCalloc(&channel->collnetPeers, 1)); +@@ -121,9 +129,11 @@ ncclResult_t initCollnetChannel(struct ncclComm* comm, int channelId, struct ncc + addr = (uintptr_t)channel->collnetDevPeers; + channel->peers[comm->nRanks] = channel->collnetPeers; + NCCLCHECK(ncclCudaMemcpyAsync((uintptr_t*)(channel->devPeers + comm->nRanks), (uintptr_t*)&addr, 1, sharedRes->deviceStream.cudaStream)); ++ channel->devPeersHostPtr[comm->nRanks] = (struct ncclDevChannelPeer*)addr; + ncclAtomicRefCountIncrement(&channel->collnetPeers->refCount); + } + ++ NCCLCHECK(ncclStrongStreamSynchronize(&sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &sharedRes->deviceStream)); + + return ncclSuccess; +@@ -156,5 +166,7 @@ ncclResult_t freeChannel(struct ncclChannel* channel, int nRanks, int collnetNRa + } + } + } ++ ++ free(channel->devPeersHostPtr); + return ncclSuccess; + } +diff --git a/src/include/comm.h b/src/include/comm.h +index e79bf54..8986f93 100644 +--- a/src/include/comm.h ++++ b/src/include/comm.h +@@ -124,6 +124,8 @@ struct ncclSharedResources { + struct ncclChannel { + struct ncclChannelPeer** peers; + struct ncclDevChannelPeer** devPeers; ++ /* devPeer pointer array used for host side access */ ++ struct ncclDevChannelPeer** devPeersHostPtr; + struct ncclRing ring; + int* devRingUserRanks; + struct ncclTree tree; +diff --git a/src/init.cc b/src/init.cc +index 1ea1d7e..309ce10 100644 +--- a/src/init.cc ++++ b/src/init.cc +@@ -437,7 +437,7 @@ static ncclResult_t devCommSetup(ncclComm_t comm) { + + NCCLCHECKGOTO(ncclCudaMemcpyAsync(devCommAndChans, &tmpCommAndChans, 1, comm->sharedRes->deviceStream.cudaStream), ret, fail); + exit: +- CUDACHECK(cudaStreamSynchronize(comm->sharedRes->deviceStream.cudaStream)); ++ NCCLCHECK(ncclStrongStreamSynchronize(&comm->sharedRes->deviceStream)); + NCCLCHECK(ncclStrongStreamRelease(ncclCudaGraphNone(), &comm->sharedRes->deviceStream)); + return ret; + fail: +diff --git a/src/transport.cc b/src/transport.cc +index f4b8a2a..9817beb 100644 +--- a/src/transport.cc ++++ b/src/transport.cc +@@ -147,11 +147,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, sendData[i] + sendDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[sendPeer]->send[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[sendPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[sendPeer]->send[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +@@ -167,11 +165,9 @@ ncclResult_t ncclTransportP2pSetup(struct ncclComm* comm, struct ncclTopoGraph* + if (conn->connected == 0) { + NCCLCHECKGOTO(conn->transportComm->connect(comm, recvData[i] + recvDataOffset++, 1, comm->rank, conn), ret, fail); + if (ret == ncclSuccess) { +- struct ncclDevChannelPeer* addr; + conn->connected = 1; + /* comm->channels[c].devPeers[recvPeer]->recv[connIndex] is a device memory access. */ +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, &comm->channels[c].devPeers[recvPeer], sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), ret, fail); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[recvPeer]->recv[connIndex], &conn->conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), ret, fail); + } else if (ret == ncclInProgress) { + allChannelsConnected = false; + } +diff --git a/src/transport/nvls.cc b/src/transport/nvls.cc +index 633cb04..07be99d 100644 +--- a/src/transport/nvls.cc ++++ b/src/transport/nvls.cc +@@ -359,12 +359,10 @@ ncclResult_t ncclNvlsSetup(struct ncclComm* comm, struct ncclComm* parent) { + peer->send[0].conn.tail = (uint64_t*)(mem + buffSize + memSize / 2); + peer->send[0].conn.flags |= NCCL_NVLS_MIN_POLL; + +- struct ncclDevChannelPeer* addr; +- CUDACHECKGOTO(cudaMemcpyAsync(&addr, comm->channels[c].devPeers + nvlsPeer, sizeof(struct ncclDevChannelPeer*), cudaMemcpyDeviceToHost, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); +- CUDACHECKGOTO(cudaMemcpyAsync(&addr->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[0], &peer->send[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[0], &peer->recv[0].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->send[1], &peer->send[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); ++ CUDACHECKGOTO(cudaMemcpyAsync(&comm->channels[c].devPeersHostPtr[nvlsPeer]->recv[1], &peer->recv[1].conn, sizeof(struct ncclConnInfo), cudaMemcpyHostToDevice, comm->sharedRes->hostStream.cudaStream), res, cleanup); + + /*INFO(NCCL_INIT|NCCL_NVLS, "Peer %d Channel %d MC buff %p/%p UC Buff %p/%p", + nvlsPeer, c, +-- +2.45.2 diff --git a/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb new file mode 100644 index 00000000000..dbc35f62054 --- /dev/null +++ b/easybuild/easyconfigs/n/NECAT/NECAT-0.0.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'NECAT' +version = '0.0.1' + +homepage = 'https://github.com/xiaochuanle/NECAT' +description = """NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/xiaochuanle/NECAT/archive/'] +sources = ['v%(version)s_update20200803.tar.gz'] +checksums = ['5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +start_dir = 'src' + +files_to_copy = [ + (['../Linux-amd64/bin/*'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.pl'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9bb438dc94 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb new file mode 100644 index 00000000000..e6ef7ccfb3e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.23.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8f7a531ce0e --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-3.1.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '3.1.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['71cd6827f20c68e384555dbcfc85422d0690e21d21d7b5d4f7375544a2755271'] + +builddependencies = [('CMake', '3.26.3')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb new file mode 100644 index 00000000000..94de23b83da --- /dev/null +++ b/easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb @@ -0,0 +1,42 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoComp' +version = '1.24.0' + +homepage = 'https://github.com/wdecoster/NanoComp' +description = "Comparing runs of Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce02bb38c76137ee00ebcc68b6b2654a4a459993e901aebde436c4d54287b09'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('NanoPlot', '1.43.0'), + ('plotly.py', '5.16.0'), + ('plotly-orca', '1.3.1'), + ('joypy', '0.2.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoComp'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoComp --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb new file mode 100644 index 00000000000..fed069c1e75 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb new file mode 100644 index 00000000000..1aef705dc4e --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb new file mode 100644 index 00000000000..1b21ec42201 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Update: Petr Král (INUITS) +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('minimap2', '2.26'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.28', { + 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'], + }), + (name, version, { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb new file mode 100644 index 00000000000..4e547b9963b --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.43.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), + ('nanoget', '1.19.3'), + ('plotly.py', '5.16.0'), + ('statsmodels', '0.14.1'), + ('Arrow', '14.0.1'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb new file mode 100644 index 00000000000..8f0fa5a053c --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'NanoStat' +version = '1.6.0' + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'] + +dependencies = [ + ('Python', '3.11.3'), + ('nanoget', '1.19.3'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..857ec88ff80 --- /dev/null +++ b/easybuild/easyconfigs/n/NextPolish/NextPolish-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'MakeCp' + +name = 'NextPolish' +version = '1.4.1' + +homepage = 'https://github.com/Nextomics/NextPolish' +description = 'NextDenovo is a string graph-based de novo assembler for long reads.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Nextomics/NextPolish/releases/download/'] +sources = [{ + 'download_filename': 'v%(version)s/%(name)s.tgz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['2a5f66f3db7f76e583a6b6e28f9c1f3c392258b8d755050d7abe129a2fbb48c4'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('BWA', '0.7.17'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Paralleltask', '0.2.3', { + 'modulename': 'paralleltask', + 'checksums': ['8015a8311d5021bc44edbfbf45ff2557a529999e235d25190bac62993fdf7b66'], + }), +] + +# fix make -C util - warning: jobserver unavailable +parallel = 1 + +# fix bwa bug - https://github.com/Nextomics/NextPolish/issues/83 +prebuildopts = "sed -i 's/seq_count bwa samtools minimap2/seq_count samtools minimap2/' Makefile && " +prebuildopts += "rm -rf util/bwa && " +prebuildopts += ( + "sed -i" + " -e 's/seq_count bwa_ samtools_/seq_count samtools_/'" + " -e '29d'" # @+make clean -C $(BWADIR) + " -e '18,20d'" # bwa_: @+make -C $(BWADIR) + " -e '1d'" # BWADIR = ./bwa + " util/Makefile && " +) +postinstallcmds = ['cd %(installdir)s/bin && ln -s $EBROOTBWA/bin/bwa'] + +files_to_copy = ['bin', 'lib', 'test_data', 'LICENSE', 'nextPolish'] + +sanity_check_paths = { + 'files': ['nextPolish', 'bin/minimap2', 'bin/paralleltask', 'bin/bwa'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['nextPolish --help'] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb new file mode 100644 index 00000000000..a930785f65b --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '5.2.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pillow', '9.4.0'), + ('pydicom', '2.4.4'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..64684d1ff42 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-8.1-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '8.1' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6508bfbcfe38153ecbdc1b7d3479323564353f134acc8c501910220371390675'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('ncurses', '6.5')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb new file mode 100644 index 00000000000..264a822a3ca --- /dev/null +++ b/easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'nanoQC' +version = '0.9.4' + +homepage = 'https://github.com/wdecoster/nanoQC' +description = """Quality control tools for long read sequencing + data aiming to replicate some of the plots made by fastQC.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'nanoQC'} + +sanity_check_commands = ["nanoQC --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb new file mode 100644 index 00000000000..2aeb2ceaf26 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.19.3' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('nanomath', '1.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb new file mode 100644 index 00000000000..2a2f56955cc --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.4.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math functions for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['ed7a38fbb156d9a68a95c2570fe3c2035321d0a3e234580496750afca4927ced'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb new file mode 100644 index 00000000000..d32ee79a46a --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.14.0' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + { + 'source_urls': ['https://github.com/jts/nanopolish/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'], + 'download_filename': 'v1.1.0.tar.gz', + 'filename': 'slow5lib-v1.1.0.tar.gz', + }, +] +checksums = [ + {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'}, + {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'}, +] + +builddependencies = [('Eigen', '3.4.0')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('Pysam', '0.22.0'), + ('HDF5', '1.14.0'), + ('HTSlib', '1.18'), + ('minimap2', '2.26'), + ('VBZ-Compression', '1.0.3'), +] + +prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..35d0c5778dd --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CUDA', '12.1.1', '', SYSTEM), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), + ('CuPy', '13.0.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb new file mode 100644 index 00000000000..34b3ce6299a --- /dev/null +++ b/easybuild/easyconfigs/n/nellie/nellie-0.3.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'nellie' +version = '0.3.1' + +homepage = 'https://github.com/aelefebv/nellie/' +description = """ +Napari plugin for automated organelle segmentation, +tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('napari', '0.4.18'), + ('scikit-image', '0.22.0'), + ('imagecodecs', '2024.1.1'), + ('matplotlib', '3.7.2'), + ('ome-types', '0.5.1.post1'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = ( + "sed -i" + " -e 's/numpy==1.26.4/numpy/'" + " -e 's/scipy==1.12.0/scipy/'" + " -e 's/nd2==0.9.0/nd2/'" + " -e 's/pandas==2.2.1/pandas/'" + " -e 's/matplotlib==3.8.3/matplotlib/'" + " -e 's/napari[all]/napari/'" + " setup.cfg && " +) + +exts_list = [ + ('resource_backed_dask_array', '0.1.0', { + 'checksums': ['8fabcccf5c7e29059b5badd6786dd7675a258a203c58babf10077d9c90ada54f'], + }), + ('nd2', '0.10.1', { + 'checksums': ['88ee60f6ba39392722a162da58fb81bf0cdb8ed6c772772e4db91e90f97e490a'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['3fd85bd1c7df5a8f24bff2118805cd7c82140b08871d520b2131d4d9a8c00d94'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef91cf135fe --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.10-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.10' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b4c518adb174e484cb4acea54118f02380c7133771e7e9beb98a0787194ee47c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8be75746afa --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.3' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e7c2035444b --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.29.2-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.29.2' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1d63e967973733d2c97e841e3c05fac4d3fa299f01d14c86f2695594c7a4a2ec'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb new file mode 100644 index 00000000000..74e99150d4b --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.9.0-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.9.0' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4df4163fcab20030137e8f2aa23e88e1e42e6fe702387cfd95d7675e1d84645e'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..91b8598722a --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + '562fc7c755393eaad9751e56149339dd201ffbfdb3ef5f43ff21d0619ba9045f', + }], + 'modulename': 'onnxruntime', + }), +] + +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + +sanity_pip_check = True + +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb new file mode 100644 index 00000000000..440ae5d93e7 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.19.2-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.19.2' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.5.26'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime-%%(version)s-cp311-cp311-manylinux_2_27_%s.manylinux_2_28_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + 'a36511dc07c5c964b916697e42e366fa43c48cdb3d3503578d78cef30417cb84', + local_whl_tmpl % ('aarch64', 'aarch64'): + 'c1dfe4f660a71b31caa81fc298a25f9612815215a47b286236e61d540350d7b6', + }], + 'modulename': 'onnxruntime', + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..503a56951d0 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.8' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb new file mode 100644 index 00000000000..ff3112bb084 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b-avx2.eb @@ -0,0 +1,37 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb new file mode 100644 index 00000000000..f28a5a3ff99 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-foss-2023b.eb @@ -0,0 +1,36 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +# optional dependency for ORCA, +# see also https://xtb-docs.readthedocs.io/en/latest/setup.html#using-xtb-with-orca +dependencies = [('xtb', '6.7.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s $EBROOTXTB/bin/xtb otool_xtb"] + +enhance_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/orca', 'bin/otool_xtb'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..cdc92c16f64 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.0' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_avx2_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz + '02c21294efe7b1b721e26cb90f98ee15ad682d02807201b7d217dfe67905a2fd', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb new file mode 100644 index 00000000000..8bf88fa8129 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.0-gompi-2023a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_0_linux_x86-64_shared_openmpi416.tar.xz + '219bd1deb6d64a63cb72471926cb81665cbbcdec19f9c9549761be67d49a29c6', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb index 6f36b886477..0d9573028dd 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024.06.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-gompi-2024a.eb @@ -6,7 +6,7 @@ version = '7.4' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'iimpi', 'version': '2024.06'} +toolchain = {'name': 'gompi', 'version': '2024a'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb new file mode 100644 index 00000000000..3122923be15 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.4-iimpi-2024a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.4' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2024a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1edd0c2efa61999409bfb28740a7f39689a5b42b1a1b4c66d1656e5637f7cefc'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb index 6e982449e9e..fe8a5244c12 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb index 7c4d60f0514..488b8e0de0d 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.9.6'), ] +local_pyshortver = '3.9' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] -sanity_check_commands = ['%(namelower)s-config --help'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb index 61eba75f5f0..6756aa72eac 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.4'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb index 54478bf62fa..f4c842e0450 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,21 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.10.8'), ] +local_pyshortver = '3.10' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb index 17595d97acb..db786b12a41 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb index 48cbf931ec5..c5108c8daca 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb @@ -3,6 +3,7 @@ # Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer +# Jan Andre Reuter # License:: 3-clause BSD # # This work is based on experiences from the UNITE project @@ -34,17 +35,22 @@ builddependencies = [ dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), ] +local_pyshortver = '3.11' configopts = '--enable-shared' +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } - -sanity_check_commands = ['%(namelower)s-config --help'] +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fdf78e0772d --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Jan André Reuter +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['otf2-3.0.3-update-py-compile.patch'] +checksums = [ + '18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8', # otf2-3.0.3.tar.gz + '5b1dad8788642eaa97bc03003c9329380340ba10649e556a30ce541165cf8da4', # otf2-3.0.3-update-py-compile.patch +] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), + # OTF2 Python bindings + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +local_pyshortver = '3.12' +configopts = '--enable-shared' + +modextrapaths = {'PYTHONPATH': ['lib64/python%s/site-packages' % local_pyshortver]} + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ['%(namelower)s-config --help', + 'python -c "import %(namelower)s"'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch new file mode 100644 index 00000000000..539726fbf14 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/otf2-3.0.3-update-py-compile.patch @@ -0,0 +1,252 @@ +This patch updates the py-compile file used by OTF2 during the install process +to fix the removal of the imp module in Python 3.12 which was long deprecated. +With this, OTF2 can be installed with Python 3.12, which would previously fail +with a module not found error. + +--- build-config/py-compile 2023-02-12 17:32:31.274132086 +0100 ++++ ../../otf2/build-config/py-compile 2024-08-22 17:44:59.939242651 +0200 +@@ -1,7 +1,7 @@ + #!/bin/sh + # py-compile - Compile a Python program + +-scriptversion=2011-06-08.12; # UTC ++scriptversion=2023-03-30.00; # UTC + + # Copyright (C) 2000-2013 Free Software Foundation, Inc. + +@@ -27,7 +27,7 @@ + # bugs to or send patches to + # . + +-if [ -z "$PYTHON" ]; then ++if test -z "$PYTHON"; then + PYTHON=python + fi + +@@ -79,13 +79,20 @@ + ;; + -h|--help) + cat <<\EOF +-Usage: py-compile [--help] [--version] [--basedir DIR] [--destdir DIR] [--silent] FILES..." ++Usage: py-compile [options] FILES... + + Byte compile some python scripts FILES. Use --destdir to specify any + leading directory path to the FILES that you don't want to include in the + byte compiled file. Specify --basedir for any additional path information you + do want to be shown in the byte compiled file. + ++Options: ++ --basedir DIR Prefix all FILES with DIR, and include in error messages. ++ --destdir DIR Prefix all FILES with DIR before compiling. ++ -v, --version Display version information. ++ -h, --help This help screen. ++ --silent Operate silently. ++ + Example: + py-compile --destdir /tmp/pkg-root --basedir /usr/share/test test.py test2.py + +@@ -114,87 +121,165 @@ + shift + done + +-files=$* +-if test -z "$files"; then +- usage_error "no files given" ++if test $# -eq 0; then ++ usage_error "no files given" + fi + + # if basedir was given, then it should be prepended to filenames before + # byte compilation. +-if [ -z "$basedir" ]; then +- pathtrans="path = file" ++if test -z "$basedir"; then ++ pathtrans="path = file" + else +- pathtrans="path = os.path.join('$basedir', file)" ++ pathtrans="path = os.path.join('$basedir', file)" + fi + + # if destdir was given, then it needs to be prepended to the filename to + # byte compile but not go into the compiled file. +-if [ -z "$destdir" ]; then +- filetrans="filepath = path" ++if test -z "$destdir"; then ++ filetrans="filepath = path" + else +- filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++ filetrans="filepath = os.path.normpath('$destdir' + os.sep + path)" ++fi ++ ++python_major=`$PYTHON -c 'import sys; print(sys.version_info[0])'` ++if test -z "$python_major"; then ++ usage_error "could not determine $PYTHON major version" + fi + ++case $python_major in ++[01]) ++ usage_error "python version 0.x and 1.x not supported" ++ ;; ++esac ++ ++python_minor=`$PYTHON -c 'import sys; print(sys.version_info[1])'` ++ ++# NB: When adding support for newer versions, prefer copying & adding new cases ++# rather than try to keep things merged with shell variables. ++ ++# First byte compile (no optimization) all the modules. ++# This works for all currently known Python versions. + $PYTHON -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'c' + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'c', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath), path) +- else: +- py_compile.compile(filepath, filepath + 'c', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" || exit $? ++ sys.stdout.write('\n')" "$@" || exit $? + +-# this will fail for python < 1.5, but that doesn't matter ... ++# Then byte compile w/optimization all the modules. + $PYTHON -O -c " +-import sys, os, py_compile, imp ++import sys, os, py_compile ++ ++try: ++ import importlib ++except ImportError: ++ importlib = None ++ ++# importlib.util.cache_from_source was added in 3.4 ++if ( ++ hasattr(importlib, 'util') ++ and hasattr(importlib.util, 'cache_from_source') ++): ++ destpath = importlib.util.cache_from_source ++else: ++ destpath = lambda filepath: filepath + 'o' + +-# pypy does not use .pyo optimization +-if hasattr(sys, 'pypy_translation_info'): ++# pypy2 does not use .pyo optimization ++if sys.version_info.major <= 2 and hasattr(sys, 'pypy_translation_info'): + sys.exit(0) + +-files = '''$files''' + silent = $silent + blu = '''$blu''' + std = '''$std''' + + if not silent: +- sys.stdout.write('Byte-compiling python modules (optimized versions)...') +-for file in files.split(): ++ sys.stdout.write('Byte-compiling python modules (optimized versions) ...\n') ++for file in sys.argv[1:]: + $pathtrans + $filetrans +- if not os.path.exists(filepath) or not (len(filepath) >= 3 +- and filepath[-3:] == '.py'): +- continue ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue + if not silent: +- sys.stdout.write(' ' + file) ++ sys.stdout.write(file + ' ') + sys.stdout.flush() + else: +- sys.stdout.write(' PYTHON {}{}{}\n'.format(blu, filepath + 'o', std)) +- if hasattr(imp, 'get_tag'): +- py_compile.compile(filepath, imp.cache_from_source(filepath, False), path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) ++if not silent: ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ++# Then byte compile w/more optimization. ++# Only do this for Python 3.5+, see https://bugs.gnu.org/38043 for background. ++case $python_major.$python_minor in ++2.*|3.[0-4]) ++ ;; ++*) ++ $PYTHON -OO -c " ++import sys, os, py_compile, importlib ++ ++destpath = importlib.util.cache_from_source ++ ++silent = $silent ++blu = '''$blu''' ++std = '''$std''' ++ ++if not silent: ++ sys.stdout.write('Byte-compiling python modules (more optimized versions)' ++ ' ...\n') ++for file in sys.argv[1:]: ++ $pathtrans ++ $filetrans ++ if ( ++ not os.path.exists(filepath) ++ or not (len(filepath) >= 3 and filepath[-3:] == '.py') ++ ): ++ continue ++ if not silent: ++ sys.stdout.write(file + ' ') ++ sys.stdout.flush() + else: +- py_compile.compile(filepath, filepath + 'o', path) ++ sys.stdout.write(' PYCACHE {}{}{}\n'.format(blu, destpath(filepath), std)) ++ py_compile.compile(filepath, destpath(filepath), path) + if not silent: +- sys.stdout.write('\n')" 2>/dev/null || : ++ sys.stdout.write('\n')" "$@" 2>/dev/null || exit $? ++ ;; ++esac + + # Local Variables: + # mode: shell-script diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..f6e66db69ae --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.4-GCCcore-13.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.4' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['81e6518f2c4656fdeaf18a018f135e96a96e7f66dbe1c1f05860dd94772176cc'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Imath', '3.1.11'), + ('zlib', '1.3.1') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..b65ce71cf76 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,66 @@ +easyblock = 'EB_OpenFOAM' + +name = 'OpenFOAM-Extend' +local_commit = 'aa97a0' +version = '4.1-20210705' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.extend-project.de/' +description = """OpenFOAM is a free, open source CFD software package. +OpenFOAM has an extensive range of features to solve anything from complex fluid flows +involving chemical reactions, turbulence and heat transfer, +to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + 'git_config': { + 'url': 'https://git.code.sf.net/p/foam-extend/', + 'repo_name': 'foam-extend-4.1', + 'commit': local_commit, + }, +}] +patches = [ + 'OpenFOAM-Extend-3.2-ParMGridGen.patch', + 'OpenFOAM-Extend-3.1_build-qa.patch', + 'OpenFOAM-Extend-4.1_comp-mpi.patch', + 'OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch', + 'OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch', +] +checksums = [ + # no checksum for OpenFOAM-Extend-4.1-20200408-f2c557.tar.gz since it's created from git repo, + # and hence resuluting tarball won't be exactly the same on all systems + None, + 'f7676a7a12ced7c74caea64c62826a28449fdb2beb8b5be2c4ae7528ffece16e', # OpenFOAM-Extend-3.2-ParMGridGen.patch + '14dcc12ea7191ba42a9c297fcb2f4fbc2c55bf57226029489aa116e2d060b4bf', # OpenFOAM-Extend-3.1_build-qa.patch + 'e71a77b6f39653f9a0d4b0ce6691433c742df74f23402782c69a8b736c98eb7a', # OpenFOAM-Extend-4.1_comp-mpi.patch + # OpenFOAM-Extend-3.1_skip-ThirdParty-OpenMPI.patch + 'c88b23cd2f5dcf3bd86e02d7ea5dc6719c2049cf4b20e39f1b3262381dee3c50', + # OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch + '47868f35d9a899047be8da451df46e165fc813bc809b96b1c35a0cccddb1a9e6', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('M4', '1.4.19'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('hwloc', '2.9.1'), + ('ParMETIS', '4.0.3'), + ('METIS', '5.1.0'), # order matters, METIS need to be listed after ParMETIS to get $CPATH right + ('SCOTCH', '7.0.3'), + ('Mesquite', '2.3.0'), + ('ParMGridGen', '1.0'), + ('Python', '2.7.18'), + # Libccmio v2.6.1, zoltan v3.5 +] + +# too many builds in parallel actually slows down the build +maxparallel = 4 + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch new file mode 100644 index 00000000000..84229fdd90a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM-Extend/OpenFOAM-Extend-4.1-20210705_fix-private-PackedList.patch @@ -0,0 +1,14 @@ +fix for: +error: class Foam::UList Foam::UList::UList is private within this context +see also https://sourceforge.net/p/foam-extend/tickets/68/ +--- foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H.orig 2024-09-12 21:13:26.103914000 +0200 ++++ foam-extend-4.1-20210705/src/foam/containers/Lists/PackedList/PackedList.H 2024-09-12 21:13:53.608924991 +0200 +@@ -147,7 +147,7 @@ + class PackedList + : + public PackedListCore, +- private List ++ public List + { + protected: + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch new file mode 100644 index 00000000000..e8a0b33adf7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-ThirdParty.patch @@ -0,0 +1,397 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham). +# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +@@ -11,8 +11,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-12-version-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt ++++ OpenFOAM-12/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-12-version-12/etc/bashrc OpenFOAM-12/etc/bashrc +--- OpenFOAM-12-version-12/etc/bashrc ++++ OpenFOAM-12/etc/bashrc +@@ -43,12 +43,13 @@ + # + [ "$BASH" ] && bashrcFile=${BASH_SOURCE} + [ "$ZSH_NAME" ] && bashrcFile=$0 +-if [ -n "$bashrcFile" ] +-then +- export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) +-else +- export FOAM_INST_DIR=$HOME/$WM_PROJECT +-fi ++#if [ -n "$bashrcFile" ] ++#then ++# export FOAM_INST_DIR=$(cd $(dirname $bashrcFile)/../.. && pwd -P) ++#else ++# export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#fi ++# For Easybuild: set by the module + unset bashrcFile + # + # Please set to the appropriate path if the above default is not correct. E.g., +diff -ru OpenFOAM-12-version-12/etc/config.sh/gperftools OpenFOAM-12/etc/config.sh/gperftools +--- OpenFOAM-12-version-12/etc/config.sh/gperftools ++++ OpenFOAM-12/etc/config.sh/gperftools +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-12-version-12/etc/config.sh/metis OpenFOAM-12/etc/config.sh/metis +--- OpenFOAM-12-version-12/etc/config.sh/metis ++++ OpenFOAM-12/etc/config.sh/metis +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the metis installation +-case "$METIS_TYPE" in +-none) +- ;; +-system) +- export METIS_VERSION=system +- export METIS_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$METIS_VERSION" ] +- then +- metisSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/metis-*) +- else +- metisSrcDir=$WM_THIRD_PARTY_DIR/metis-$METIS_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$metisSrcDir" ] +- then +- export METIS_VERSION=${metisSrcDir##*metis-} +- export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/metis-$METIS_VERSION +- fi +- # Clean up +- unset metisSrcDir +- ;; +-esac ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/mpi OpenFOAM-12/etc/config.sh/mpi +--- OpenFOAM-12-version-12/etc/config.sh/mpi ++++ OpenFOAM-12/etc/config.sh/mpi +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-12-version-12/etc/config.sh/paraview OpenFOAM-12/etc/config.sh/paraview +--- OpenFOAM-12-version-12/etc/config.sh/paraview ++++ OpenFOAM-12/etc/config.sh/paraview +@@ -38,117 +38,13 @@ + ) \ + && PATH="$cleaned" + +-# Detect the most recent version of cmake available and add to the PATH +-cmakeDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/cmake-*) +-if [ -n "$cmakeDir" ] +-then +- export PATH=$cmakeDir/bin:$PATH +-fi +-unset cmakeDir +- +-# Set up the paraview environment +-case "$ParaView_TYPE" in +-none) +- ;; +- +-system) +- +- # Look for a paraview installation +- if pvserverExe=$(which pvserver 2> /dev/null) +- then +- paraviewBinDir=$(dirname $pvserverExe) +- paraviewBinDir=$(cd $paraviewBinDir && pwd -P) +- fi +- +- # Set the environment +- if [ -d "$paraviewBinDir" ] +- then +- export ParaView_DIR=$(dirname $paraviewBinDir) +- export ParaView_LIB_DIR=$(unset LD_LIBRARY_PATH && \ +- ldd $paraviewBinDir/paraview | \ +- grep -o "/.*/libpqCore-pv.*.so" | \ +- xargs dirname) +- export ParaView_VERSION=$(unset LD_LIBRARY_PATH && \ +- pvserver --version 2> /dev/null | \ +- awk '{print $NF}') +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the library path +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset pvserverExe paraviewBinDir +- ;; +- +-paraviewopenfoam) +- +- # Look for a paraview installation. The version should be set externally. +- if [ -n "$ParaView_VERSION" ] +- then +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- paraviewDir=/opt/paraviewopenfoam$(echo "$ParaView_MAJOR" | tr -d '.') +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- fi +- +- unset paraviewDir +- ;; +- +-OpenFOAM | ThirdParty) +- +- # Look for a paraview installation +- if [ -z "$ParaView_VERSION" ] +- then +- paraviewDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/platforms/$WM_ARCH$WM_COMPILER/ParaView-*) +- else +- paraviewDir=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION +- fi +- +- # Set the environment +- if [ -d "$paraviewDir" ] +- then +- export ParaView_DIR=$paraviewDir +- export ParaView_LIB_DIR=$(echo "$ParaView_DIR"/lib* | tr ' ' ':') +- export ParaView_VERSION=${paraviewDir##*ParaView-} +- export ParaView_MAJOR=${ParaView_VERSION%.*} +- export ParaView_INCLUDE_DIR=$paraviewDir/include/paraview-$ParaView_MAJOR +- export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR +- +- # Add to the path and the library path +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH +- +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r "$paraviewPython" ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- unset paraviewPython +- fi +- +- unset paraviewDir +- ;; +- +-esac ++export ParaView_VERSION=$EBVERSIONPARAVIEW ++export ParaView_MAJOR=${ParaView_VERSION%.*} ++export ParaView_DIR=$EBROOTPARAVIEW ++export ParaView_LIB_DIR=$ParaView_DIR/lib ++export ParaView_INCLUDE_DIR=$ParaView_DIR/include/paraview-$ParaView_MAJOR ++export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR ++export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$PV_PLUGIN_PATH:$LD_LIBRARY_PATH + + # Report + if [ "$FOAM_VERBOSE" ] && [ "$PS1" ] && [ -d "$ParaView_DIR" ] +diff -ru OpenFOAM-12-version-12/etc/config.sh/scotch OpenFOAM-12/etc/config.sh/scotch +--- OpenFOAM-12-version-12/etc/config.sh/scotch ++++ OpenFOAM-12/etc/config.sh/scotch +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the scotch installation +-case "$SCOTCH_TYPE" in +-none) +- ;; +-system) +- export SCOTCH_VERSION=system +- export SCOTCH_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$SCOTCH_VERSION" ] +- then +- scotchSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/scotch_*) +- else +- scotchSrcDir=$WM_THIRD_PARTY_DIR/scotch_$SCOTCH_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$scotchSrcDir" ] +- then +- export SCOTCH_VERSION=${scotchSrcDir##*scotch_} +- export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/scotch_$SCOTCH_VERSION +- fi +- # Clean up +- unset scotchSrcDir +- ;; +-esac ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/zoltan OpenFOAM-12/etc/config.sh/zoltan +--- OpenFOAM-12-version-12/etc/config.sh/zoltan ++++ OpenFOAM-12/etc/config.sh/zoltan +@@ -37,32 +37,8 @@ + # Load functions + . $WM_PROJECT_DIR/etc/config.sh/functions + +-# Find the path to the zoltan installation +-case "$ZOLTAN_TYPE" in +-none) +- ;; +-system) +- export ZOLTAN_VERSION=system +- export ZOLTAN_ARCH_PATH=/usr +- ;; +-OpenFOAM | ThirdParty) +- # Look for the source directory +- if [ -z "$ZOLTAN_VERSION" ] +- then +- zoltanSrcDir=$(_foamMostRecentDir "$WM_THIRD_PARTY_DIR"/Zoltan-*) +- else +- zoltanSrcDir=$WM_THIRD_PARTY_DIR/Zoltan-$ZOLTAN_VERSION +- fi +- # Set the version and the installation path +- if [ -d "$zoltanSrcDir" ] +- then +- export ZOLTAN_VERSION=${zoltanSrcDir##*Zoltan-} +- export ZOLTAN_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/Zoltan-$ZOLTAN_VERSION +- fi +- # Clean up +- unset zoltanSrcDir +- ;; +-esac ++export ZOLTAN_VERSION=Zoltan-$EBVERSIONZOLTAN ++export ZOLTAN_ARCH_PATH=$EBROOTZOLTAN + + # Unload functions + . $WM_PROJECT_DIR/etc/config.sh/functions +diff -ru OpenFOAM-12-version-12/etc/config.sh/settings OpenFOAM-12/etc/config.sh/settings +--- OpenFOAM-12-version-12/etc/config.sh/settings ++++ OpenFOAM-12/etc/config.sh/settings +@@ -63,11 +63,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/Make/options +@@ -6,15 +6,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(PTSCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- $(if $(PTSCOTCH_LIB_DIR),-L$(PTSCOTCH_LIB_DIR)) \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +--- OpenFOAM-12-version-12/src/parallel/decompose/ptscotch/ptscotch.C ++++ OpenFOAM-12/src/parallel/decompose/ptscotch/ptscotch.C +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++#include ++ + extern "C" + { + #include +- #include +- #include "ptscotch.h" + } + +diff -ru OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options OpenFOAM-12/src/parallel/decompose/scotch/Make/options +--- OpenFOAM-12-version-12/src/parallel/decompose/scotch/Make/options ++++ OpenFOAM-12/src/parallel/decompose/scotch/Make/options +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I$(or $(SCOTCH_INCLUDE_DIR),/usr/include/scotch) \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb new file mode 100644 index 00000000000..ed565315859 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-12-foss-2023a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '12' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'vectorize': False} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-12-ThirdParty.patch'] +checksums = [ + {'version-12.tar.gz': 'e59fad54c62e64f1bb89dbaebe5f99a76dc0a6a91d9aad86042a7c4cef6d0744'}, + {'OpenFOAM-12-ThirdParty.patch': 'b8a9abf3b8479d32d87654d833501f54abe57ceb9f06f7d2412a3e52d20108ec'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), + ('Zoltan', '3.901'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch new file mode 100644 index 00000000000..ac5229788c5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-cleanup.patch @@ -0,0 +1,182 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# +# ChangeLog: +# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup +# author: Jiri Furst +# - v2406 - set MPFR_ARCH_PATH and GMP_ARCH_PATH to CGAL config +# author: Jiri Furst +# +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,8 @@ ++##Easybuild## settings -*- sh -*- ++ ++export MPFR_ARCH_PATH="$EBROOTMPFR" ++export GMP_ARCH_PATH="$EBROOTGMP" ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ +--- OpenFOAM-v2312/etc/config.sh/setup.orig 2024-01-11 09:49:24.823571481 +0100 ++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100 +@@ -207,7 +207,9 @@ + _foamEtc -config CGAL + _foamEtc -config scotch + _foamEtc -config FFTW +- ++_foamEtc -config metis ++_foamEtc -config kahip ++_foamEtc -config readline + + # Finalize library paths + # ~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb new file mode 100644 index 00000000000..0e2885c064f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2406-foss-2023a.eb @@ -0,0 +1,55 @@ +name = 'OpenFOAM' +version = 'v2406' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++14', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [ + SOURCE_TGZ, + { + 'filename': '%(name)s-plugins-%(version)s.tgz', + 'extract_cmd': 'tar --strip-components=1 -C %(installdir)s/%(name)s-%(version)s/ -xzf %s' + } +] +patches = [ + ('OpenFOAM-v2406-cleanup.patch', 1), + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), +] +checksums = [ + {'OpenFOAM-v2406.tgz': '8d1450fb89eec1e7cecc55c3bb7bc486ccbf63d069379d1d5d7518fa16a4686a'}, + {'OpenFOAM-plugins-v2406.tgz': '1d008f86fad06a4a568d194c6e3d5ab52be2b20c83a3b9b1b0230e2de2d0558b'}, + {'OpenFOAM-v2406-cleanup.patch': '3abff48a517fb63719ad57fa32af746bc379a1e80c72d3e5852aa17cd13cf03e'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '241dc4898c22aab0cbd10c1ea931a07a786508ee03462d45dbc1c202fee3ebe8'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.16'), + ('CGAL', '5.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..f323c61f065 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'OpenForceField-Toolkit' +version = '0.16.0' + +homepage = 'https://github.com/openforcefield/openff-toolkit' +description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, +parameterization engine, and other tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('typing-extensions', '4.9.0'), + ('pydantic', '2.5.3'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('PyYAML', '6.0'), + ('RDKit', '2024.03.3'), + ('MDTraj', '1.9.9'), + ('JupyterNotebook', '7.0.2'), + ('AmberTools', '23.6'), + ('Pint', '0.23'), + ('nglview', '3.1.2'), +] + +use_pip = True + +exts_list = [ + ('qcelemental', '0.26.0', { + 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('apsw', '3.46.0.0', { + 'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'], + }), + ('zstandard', '0.18.0', { + 'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'], + }), + ('qcportal', '0.55', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('bson', '0.5.10', { + 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('intermol', '0.1.2', { + 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], + }), + ('SMIRNOFF99Frosst', '1.1.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], + }), + ('SMIRNOFF-Plugins', '2024.01.0', { + 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], + }), + ('OpenForceField-ForceFields', '2024.04.0', { + 'modulename': 'openforcefields', + 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], + }), + ('OpenForceField-Amber-FF-Ports', '0.0.4', { + 'modulename': 'openff.amber_ff_ports', + 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], + }), + ('OpenForceField-Utilities', '0.1.12', { + 'modulename': 'openff.utilities', + 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], + }), + ('OpenForceField-Units', '0.2.2', { + 'modulename': 'openff.units', + 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], + }), + ('OpenForceField-NAGL-Models', '0.2.0', { + 'modulename': 'openff.nagl_models', + 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'], + }), + ('OpenForceField-Models', '0.1.2', { + 'modulename': 'openff.models', + 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], + }), + ('OpenForceField-Interchange', '0.3.27', { + 'modulename': 'openff.interchange', + 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], + }), + (name, version, { + 'modulename': 'openff.toolkit', + 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], + }), +] + +sanity_check_commands = [ + "python -c 'from openff.toolkit import Molecule, Topology, ForceField'", + "python -c 'from openff.interchange import Interchange'", + "python -c 'from openff.units import unit'", + "python -c 'from openff.interchange.components.mdconfig import MDConfig'", + "python -c 'from openff.interchange.models import TopologyKey'", + "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8ee5d1477f8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.2-GCCcore-13.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.2' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90e3896fed910c376aaf79cdd98bdfdaf98c6472efd8e1debf0a854938cbda6a'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), + ('LibTIFF', '4.6.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8cf271071e7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,70 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cbf6bca94d7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb new file mode 100644 index 00000000000..a8bdbafa429 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.10.3'), + ('SQLite', '3.39.4'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.10'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index b013362d2e5..50dab938d40 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.35')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb index e590dd730ca..d92bda87180 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb @@ -16,9 +16,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.37')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -121,7 +121,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 6b695f63279..bdf0b5c45a6 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -15,9 +15,9 @@ dependencies = [ ] builddependencies = [('binutils', '2.39')] -exts_default_options = { - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True + exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], @@ -114,7 +114,6 @@ exts_list = [ }), ] -sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..61000b1388c --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + ('optax', version, { + 'checksums': ['f09bf790ef4b09fb9c35f79a07594c6196a719919985f542dc84b0bf97812e0e'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb similarity index 71% rename from easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb rename to easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb index be05f009e9e..d447a77bbd2 100644 --- a/easybuild/easyconfigs/o/Optax/Optax-0.2.2-foss-2023a.eb +++ b/easybuild/easyconfigs/o/Optax/Optax-0.2.2-gfbf-2023a.eb @@ -6,7 +6,7 @@ version = '0.2.2' homepage = 'https://github.com/deepmind/optax' description = """Optax is a gradient processing and optimization library for JAX.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), @@ -20,13 +20,6 @@ exts_list = [ ('toolz', '0.12.1', { 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], }), - ('flit_core', '3.9.0', { - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), ('chex', '0.1.86', { 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], }), diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb new file mode 100644 index 00000000000..35dec40e234 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.6.1-foss-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.6.1' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('SciPy-bundle', '2023.11'), + ('tqdm', '4.66.2'), + ('matplotlib', '3.8.2'), # optional + ('plotly.py', '5.18.0'), # optional + ('redis-py', '5.0.9'), # optional + ('scikit-learn', '1.4.0'), # optional + ('SQLAlchemy', '2.0.29'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmaes', '0.11.1', { + 'checksums': ['cf71fa3679814723be771f2c9edd85f465b1bc1e409e1ad6d8a9e481efcd5160'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['146e530b57b4b9afd7526b3e642fbe65491f7e292b405913355f8e438e361ecf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb new file mode 100644 index 00000000000..0de34e3542b --- /dev/null +++ b/easybuild/easyconfigs/o/ome-types/ome-types-0.5.1.post1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ome-types' +version = '0.5.1.post1' + +homepage = 'https://github.com/tlambert03/ome-types/' +description = """ +ome_types provides a set of python dataclasses and utility functions for parsing +the OME-XML format into fully-typed python objects for interactive or programmatic access in python. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('hatchling', '1.18.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('pydantic', '2.5.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ruff', '0.3.0', { + 'checksums': ['0886184ba2618d815067cf43e005388967b67ab9c80df52b32ec1152ab49f53a'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('untokenize', '0.1.1', { + 'checksums': ['3865dbbbb8efb4bb5eaa72f1be7f3e0be00ea8b7f125c69cbd1f5fda926f37a2'], + }), + ('docformatter', '1.7.5', { + 'checksums': ['ffed3da0daffa2e77f80ccba4f0e50bfa2755e1c10e130102571c890a61b246e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('xsdata', '23.8', { + 'checksums': ['55f03d4c88236f047266affe550ba0dd19476adfce6a01f3e0aefac7c8078e56'], + }), + ('ome_types', version, { + 'checksums': ['cadda5e36ad4d33dad2034fd43f32113a736fe47c67fd9e06bbb8d3858d1dc58'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bbbaa753b40 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.3.1' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5c653a9d515 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_add_initial_riscv_support.patch'] +checksums = [ + '5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f', + {'PAPI-7.1.0_add_initial_riscv_support.patch': '6c7d0d63ccf2b8c46f2ed736fbd4c58303038fb2a45315aed94c026b773af35a'} +] + +builddependencies = [ + ('binutils', '2.42'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb new file mode 100644 index 00000000000..d534bfa0f78 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-1.2-gfbf-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PCAngsd' +version = '1.2' + +homepage = "https://www.popgen.dk/software/index.php/PCAngsd" +description = "Framework for analyzing low depth NGS data in heterogeneous populations using PCA." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Cython', '3.0.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Rosemeis/pcangsd/archive/refs/tags/'], + 'checksums': ['286f09851c37e380c9abf5859595e7cd0ad8cb49f1d48b1b0ae409aab0eae62e'], + }), +] + +sanity_check_commands = [ + 'pcangsd --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..74328c99ae7 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.2' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work +download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " + + "and rename to " + sources[0]) +checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe'] + +builddependencies = [ + ('binutils', '2.42'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..b5747815246 --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000-foss-2023a-R-4.3.2.eb @@ -0,0 +1,217 @@ +easyblock = 'Bundle' + +name = 'PEcAn' +version = '1.8.0.9000' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/PecanProject/pecan' +description = """Ecosystem science, policy, and management informed by the best available data and models.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('PostgreSQL', '16.1'), + ('CDO', '2.2.2'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.2'), + ('UDUNITS', '2.2.28'), + ('texlive', '20230313'), + ('NCO', '5.1.9'), + ('ncview', '2.1.8'), + ('rjags', '4-15', versionsuffix), + ('Redland', '1.0.17'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://pecanproject.r-universe.dev/src/contrib/', # PEcAn sources + ], +} + +exts_list = [ + ('PEcAn.logger', '1.8.2.9000', { + 'checksums': ['1092f72fa63d58d83ca939a06bfa51ad3b3b4cd94ca4e68202cdb08fd3ada099'], + }), + ('PEcAn.remote', version, { + 'checksums': ['b3c7208c85d37aa6c12ca99182262a9886e57e2591faefd909232b8c89111b20'], + }), + ('PEcAn.utils', version, { + 'checksums': ['524c3231a21a1e5fc48ebc53d17e49c82f018b87c274095cd0362103fe322ec5'], + }), + ('PEcAn.DB', version, { + 'checksums': ['9b7e9b40a07879c1265d9ab6087b7448dfd34c3601c64ddcb41511c97399fece'], + }), + ('PEcAn.settings', version, { + 'checksums': ['555a7d81eec7e97b8457cef51888087af6b5d7d07f527ca58cbab07ed847fabc'], + }), + ('PEcAn.MA', '1.7.3.9000', { + 'checksums': ['680290e0ee52526db1242d95c4ca06a1e0ad117337ff721d79387797bc7e40ed'], + }), + ('PEcAn.emulator', version, { + 'checksums': ['68944ebdf1f37ff84f9b09bf02c709de9eda823728bbdea073a36d7ef19cfb9c'], + }), + ('PEcAn.priors', '1.7.3.9000', { + 'checksums': ['e942a31ae02af61b1b8e36d1c5df58f39829b3d0c29421edc151f2f063ff4c1f'], + }), + ('PEcAn.uncertainty', version, { + 'checksums': ['65e392536e17e1de2bf8f66c2cd8f46fcb26dcb3294acf0132551b6736722196'], + }), + ('amerifluxr', '1.0.0', { + 'checksums': ['ec54dce4b8e4108832eaadb60f7ef8ad28b459d3381316537492dcd755d83b25'], + }), + ('geonames', '0.999', { + 'checksums': ['1dd7bbd82d9425d14eb36f8e5bf431feaccfe3b0c4e70bf38f44f13dfc59e17b'], + }), + ('solartime', '0.0.2', { + 'checksums': ['5dd7a28db2bd4881ab740cd7004b88cd05c61e0954e3a10c8e18ebbe07d3e7d1'], + }), + ('bigleaf', '0.8.2', { + 'checksums': ['e41d82fb6298150c46f57128e959a1f1c6cfa55e916c32544bab7be69b0b6df7'], + }), + ('REddyProc', '1.3.3', { + 'checksums': ['3f673bd24f41813f631bf25139c9595bd91483e898ec31b7207c4eb8b7ff486b'], + }), + ('suntools', '1.0.0', { + 'checksums': ['42b7b39bd23ad48ded002150a0e7798fab94ed9828e5b5fdd8e5e1c9040697e2'], + }), + ('fauxpas', '0.5.2', { + 'checksums': ['84d07361a146b419cb1dcb7751654e3d5f159cf2704faf498e5ea56c8de61ef6'], + }), + ('nneo', '0.1.0', { + 'checksums': ['ca503e78cf4f4c85de6e18ad3ffde0c08d6a507ff5dc5ff91a50b3e04bf84a49'], + }), + ('PEcAn.data.atmosphere', version, { + 'checksums': ['28fb884cdeeff6405252352a261c3a884ad33202e556e88cee262aba96e1aea4'], + }), + ('redland', '1.0.17-18', { + 'checksums': ['e999ba22321733df7ed056f528e38fc4be535d36bbac8106395c14f9f60a75a0'], + }), + ('datapack', '1.4.1', { + 'checksums': ['6149733ae90e6bbbb53d5f85ca29cec5f811825e794b56029b7f325de6637493'], + }), + ('dplR', '1.7.7', { + 'checksums': ['0e35a4d2a22773499f9e4592d1a198a08c9842388ce1e5a35394990ed4cdb2bd'], + }), + ('neonUtilities', '2.4.2', { + 'checksums': ['37b4efd0ed3b724de999d08d4d430954a6c717b1d943bc84c513c4fe8dbca057'], + }), + ('storr', '1.2.5', { + 'checksums': ['4224c3991d9c043a45ce530d0698d7f2cdca231b26fe31b45e0db865026e5f63'], + }), + ('thor', '1.1.5', { + 'checksums': ['99802d8c8471ce351403f8428c1efab48ccf20f359fbd368db84f25ef8f7ecae'], + }), + ('duckdb', '1.0.0-2', { + 'patches': ['PEcAn-1.8.0.9000_duckdb.patch'], + 'checksums': [ + {'duckdb_1.0.0-2.tar.gz': '3735d51f22d62a7411aa514142cd569ce28bdaec4eb58d5f0893a476b9ccbf01'}, + {'PEcAn-1.8.0.9000_duckdb.patch': 'fb47b668b23e6c9274ce5365725af71e56f2d99771efdd343dc4283f68ab0c21'}, + ], + }), + ('duckdbfs', '0.0.4', { + 'checksums': ['90b2aff2bdefff1db4f855e2a9c9b19a404f522027105424aebd3c7e45944334'], + }), + ('neonstore', '0.5.1', { + 'checksums': ['f911e957861d558adead8ca77e4d1575a47dceb9553f1aa9d818460126deab9b'], + }), + ('HDInterval', '0.2.4', { + 'checksums': ['bb07f0edd660a02ed18e578c2798eb8c2db0e181a5e0c3e23db182d13e9494f6'], + }), + ('kknn', '1.3.1', { + 'checksums': ['22840e70ec2afa40371e274b583634c8f6d27149a87253ee411747d5db78f3db'], + }), + ('timeSeries', '4032.109', { + 'checksums': ['5e0c47584e0b01ea4011ed5ced217d95f8bb872611f6b029b0797d95eebd731f'], + }), + ('gss', '2.2-7', { + 'checksums': ['3b13144702c570c83462b4ea2ad17f4bd630cff5bf2ab0347a33c7e86a4f3f6a'], + }), + ('fBasics', '4032.96', { + 'checksums': ['e1556909871c836668b10bf90e1676aac6a2892a04663d7ab00c22a64c0b8690'], + }), + ('rmutil', '1.1.10', { + 'checksums': ['819fd7ce695cc742b4594705986eb06764460fc88521ea32de793c49de7ca5f9'], + }), + ('stable', '1.1.6', { + 'checksums': ['2238788a35b5aa9e175ad7b92348640c3dcad68b6ab0a0bc04aeec9084d29da4'], + }), + ('statip', '0.2.3', { + 'checksums': ['56a81a1882856cd1c5711ba133417b64f09071dda356e74280a0dba0db60d54f'], + }), + ('modeest', '2.4.0', { + 'checksums': ['1a949409bf64679d32400d20aa3d53e65a9a20f5bd1a40993b95f81100e0ed20'], + }), + ('runjags', '2.2.2-4', { + 'checksums': ['6f656e4d0620c0806e596ddb4bfec3934534ec17c02da699fcbfd6720a6f424f'], + }), + ('swfscMisc', '1.6.5', { + 'checksums': ['a49cb390643c4079f02986862eb2dfd33db4e6b6498e849bb418f73ffd6882e1'], + }), + ('CDM', '8.2-6', { + 'checksums': ['144a85e36c120e9f8a5bd35c1db50cf089ea4807721ac14460137b9a4b1c98d1'], + }), + ('TAM', '4.2-21', { + 'checksums': ['0d1782e42e89c1863edab12c1861d0e2628ea9ee1a1e37d268f27a3deaf3d568'], + }), + ('pbv', '0.5-47', { + 'checksums': ['e17a04efa96a601ab72172b59f555f36d28bb824f02f363cc5806b05d7d7c792'], + }), + ('sirt', '4.1-15', { + 'checksums': ['c12ffcb83bea5b549c7a34c12561f3e57798b83d68a887c5da0d9a66efac3066'], + }), + ('hoardr', '0.5.4', { + 'checksums': ['4e031ac1317584451c09bc8288ed73fb2d6ceea3c10d29dbb4be08157e489a37'], + }), + ('traits', '0.5.1', { + 'checksums': ['3080887a454d69814cd6cb9683a6750db02cf4c77b40b022ef50d40171ba6aca'], + }), + ('SimilarityMeasures', '1.4', { + 'checksums': ['b26bbc3a402d21f030cc8e4ff6baca644eb4c63a4fb33423dbc9436229a393f0'], + }), + ('PEcAn.benchmark', '1.7.3.9000', { + 'checksums': ['2e8b285869b4df148228cdde5de44a67dfe0b584b2a7cd614280134259e33ed4'], + }), + ('PEcAn.visualization', version, { + 'checksums': ['f77dcb756871a419a85e46cde4a1fb0a1993c29cce8578255d5a46db722ece43'], + }), + ('PEcAn.data.land', version, { + 'checksums': ['19c572e95c11362f4714d9c3d9cc7b2d17c2e3a34513c7ed629e7bdb99bdd0ec'], + }), + ('MODISTools', '1.1.5', { + 'checksums': ['0a6b3762865424e299e1a5ec28de78b8dcca3f673e61f42a37dae19ed78db3e3'], + }), + ('PEcAn.data.remote', version, { + 'checksums': ['c097d9395d9dbb6c123f404525cae7fdb1a99b142b32c1a40b0143060444e184'], + }), + ('SparseGrid', '0.8.2', { + 'checksums': ['1d84ae83db2a390b111589a10570d55b378c2dd3310d3bc588a94ab8845cfd14'], + }), + ('lqmm', '1.5.8', { + 'checksums': ['11eddeeeed6b9d3190a80a3b3cc3d64519c6e9cb208746a3736139340df691fb'], + }), + ('PEcAn.workflow', version, { + 'checksums': ['91a1849c040089da1088c02469b973a5f301a419237db7c840fe4ca2922f4b9d'], + }), + ('PEcAn.assim.batch', version, { + 'checksums': ['a1403a5a4591791e37e7e48ca9e9d49f66f4270757711b68b72fd38aadd411cb'], + }), + ('PEcAn.all', version, { + 'checksums': ['6fe594fb890b5680977d1bf58232b941c6d522456e7803e3dc9c4418b92db737'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s.all'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch new file mode 100644 index 00000000000..940992bf5ba --- /dev/null +++ b/easybuild/easyconfigs/p/PEcAn/PEcAn-1.8.0.9000_duckdb.patch @@ -0,0 +1,16 @@ +Fixes the `prefix_back_ was not declared` error, see https://github.com/duckdb/duckdb/pull/12344 +Source: https://patch-diff.githubusercontent.com/raw/duckdb/duckdb/pull/12344.diff +diff -u src/duckdb/third_party/re2/re2/prog.cc.orig src/duckdb/third_party/re2/re2/prog.cc +--- src/duckdb/third_party/re2/re2/prog.cc.orig 2024-07-19 14:46:13.000000000 +0200 ++++ src/duckdb/third_party/re2/re2/prog.cc 2024-08-21 15:51:17.394266979 +0200 +@@ -1143,8 +1143,8 @@ + const __m256i* bp = reinterpret_cast( + reinterpret_cast(data) + prefix_size_-1); + const __m256i* endfp = fp + size/sizeof(__m256i); +- const __m256i f_set1 = _mm256_set1_epi8(prefix_front_); +- const __m256i b_set1 = _mm256_set1_epi8(prefix_back_); ++ const __m256i f_set1 = _mm256_set1_epi8(prefix_front_back.prefix_front_); ++ const __m256i b_set1 = _mm256_set1_epi8(prefix_front_back.prefix_back_); + do { + const __m256i f_loadu = _mm256_loadu_si256(fp++); + const __m256i b_loadu = _mm256_loadu_si256(bp++); diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb new file mode 100644 index 00000000000..51357650dbb --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb @@ -0,0 +1,22 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.90-beta-7.4-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/1.9/' +description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' + +toolchain = SYSTEM + +source_urls = ['https://s3.amazonaws.com/plink1-assets/'] +sources = ['plink_linux_x86_64_20240818.zip'] +checksums = ['0ac294ffcd5d82f5b0d2d7f579ac85a87017f6fc46485b21793f5aff9c719e3d'] + +sanity_check_paths = { + 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'], + 'dirs': [], +} + +sanity_check_commands = ["plink --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a5620c426d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-13.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1307155f8f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.4.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ffe20170ee2b952207adf8a195e2141eab12cda181e49fdeb54425d98c7171d7'] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('googletest', '1.15.2'), +] + +dependencies = [ + ('SQLite', '3.45.3'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), + ('nlohmann_json', '3.11.3'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..cfbbc1eb16b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.54.0-GCCcore-13.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.54.0' + +homepage = 'https://pango.gnome.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8a9eed75021ee734d7fc0fdf3a65c3bba51dfefe4ae51a9b414a60c70b2d1ed8'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('GObject-Introspection', '1.80.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('GLib', '2.80.4'), + ('cairo', '1.18.0'), + ('HarfBuzz', '9.0.0'), + ('FriBidi', '1.0.15'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb new file mode 100644 index 00000000000..f82b44f3ee5 --- /dev/null +++ b/easybuild/easyconfigs/p/Panoply/Panoply-5.5.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PackedBinary' + +name = 'Panoply' +version = '5.5.1' + +homepage = 'https://www.giss.nasa.gov/tools/panoply' +description = "Panoply plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets." + + +toolchain = SYSTEM + +source_urls = ['https://www.giss.nasa.gov/tools/panoply/download/'] +sources = ['%(name)sJ-%(version)s.tgz'] +checksums = ['14196be2dd83721e475dfa0b230859b9e102bfdcc62119536ececbf8dcbbbb96'] + +dependencies = [ + ('Java', '11', '', SYSTEM), +] + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'mv %(installdir)s/panoply.sh %(installdir)s/bin', + 'sed -i "s,jars,../jars,g" %(installdir)s/bin/panoply.sh', + 'ln -s %(installdir)s/bin/panoply.sh %(installdir)s/bin/panoply', +] + +sanity_check_paths = { + 'files': ['bin/panoply'], + 'dirs': ['jars'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb new file mode 100644 index 00000000000..bee93301eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'ParMGridGen' +version = '1.0' + +homepage = 'http://www-users.cs.umn.edu/~moulitsa/software.html' +description = """ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, + that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited + for geometric multigrid methods.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://download.sourceforge.net/foam-extend/ThirdParty'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ParMGridGen-%(version)s_malloc_include.patch', + 'ParMGridGen-%(version)s_gompiOpenFOAM-Extend.patch', +] +checksums = [ + '62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395', # ParMGridGen-1.0.tar.gz + '3e0d72f82b3b56cbfcb1e3c9afc6594eb25316a0faeb49237faa8d969b4daeaa', # ParMGridGen-1.0_malloc_include.patch + '60cc46d156e99101b21bde9d23cf6c2db3dcdef1704f1830a7baa0320003c02a', # ParMGridGen-1.0_gompiOpenFOAM-Extend.patch +] + +buildopts = 'parallel make=make CC="$CC" PARCC="$CC" PARLD="$CC" COPTIONS="$CFLAGS" LDOPTIONS="$CFLAGS" BINDIR="."' + +files_to_copy = [ + (['MGridGen/Programs/mgridgen', 'ParMGridGen/Programs/parmgridgen'], 'bin'), + (['mgridgen.h', 'parmgridgen.h', 'MGridGen/IMlib/IMlib.h'], 'include'), + (['libmgrid.a', 'libMGridGen.a', 'libparmgrid.a', 'MGridGen/IMlib/libIMlib.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mgridgen', 'bin/parmgridgen', 'include/mgridgen.h', 'include/parmgridgen.h', + 'include/IMlib.h', 'lib/libmgrid.a', 'lib/libMGridGen.a', 'lib/libparmgrid.a', 'lib/libIMlib.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb new file mode 100644 index 00000000000..abec428859f --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b-Qt5.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.12.0' +versionsuffix = '-Qt5' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), + ('XZ', '5.4.4'), + ('HDF5', '1.14.3'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('Qt5', '5.15.13'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb index 018edd70431..ed8408c9301 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -12,11 +12,15 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +patches = [ + 'ParaView-5.11.1-remove_glew_init_warning.patch', + 'ParaView-5.12.0-qt6_fixes.patch', +] checksums = [ {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, + {'ParaView-5.12.0-qt6_fixes.patch': '015d07ac6b74c7355b56ed7f67166f0d5b765f9d6ac135b7246a675a317063df'}, ] builddependencies = [('CMake', '3.27.6')] @@ -58,7 +62,9 @@ _copts = [ '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, '-DVTK_OPENGL_HAS_EGL=ON', '-DVTK_USE_X=ON', - '-DVTK_OPENGL_HAS_OSMESA=OFF'] + '-DVTK_OPENGL_HAS_OSMESA=OFF', + '-DVTK_PYTHON_OPTIONAL_LINK=OFF'] + configopts = ' '.join(_copts) sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch new file mode 100644 index 00000000000..838d6fe5d32 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-qt6_fixes.patch @@ -0,0 +1,126 @@ +This patch solves qt6 compatibility issues. For details see +https://gitlab.kitware.com/paraview/paraview/-/merge_requests/6836 + +diff --git a/Plugins/CAVEInteraction/pqVRDockPanel.cxx b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +index 7a3d352b993f2930716b47dd98512ca88697374c..448ac4d3833ec1582d99139b3f3fea6bbdf7d3ce 100644 +--- a/Plugins/CAVEInteraction/pqVRDockPanel.cxx ++++ b/Plugins/CAVEInteraction/pqVRDockPanel.cxx +@@ -159,8 +159,8 @@ void pqVRDockPanel::initStyles() + this->Internals->stylesCombo->addItem(QString::fromStdString(styleDescs[i])); + } + +- connect(this->Internals->stylesCombo, SIGNAL(currentIndexChanged(QString)), this, +- SLOT(styleComboChanged(QString)), Qt::UniqueConnection); ++ QObject::connect(this->Internals->stylesCombo, &QComboBox::currentTextChanged, this, ++ &pqVRDockPanel::styleComboChanged, Qt::UniqueConnection); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqCustomFilterDefinitionWizard.cxx b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +index 9c140a37abca11b19f0c04bf7c41645b756457d6..acd7bd99e19017a5557a41c4585586b39e5ffc58 100644 +--- a/Qt/Components/pqCustomFilterDefinitionWizard.cxx ++++ b/Qt/Components/pqCustomFilterDefinitionWizard.cxx +@@ -134,8 +134,8 @@ pqCustomFilterDefinitionWizard::pqCustomFilterDefinitionWizard( + SLOT(clearNameOverwrite(const QString&))); + + // When combo selection changes, update new label to be same as old. +- QObject::connect(this->Form->PropertyCombo, SIGNAL(currentIndexChanged(const QString&)), +- this->Form->PropertyName, SLOT(setText(const QString&))); ++ QObject::connect(this->Form->PropertyCombo, &QComboBox::currentTextChanged, ++ this->Form->PropertyName, &QLineEdit::setText); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqDataInformationWidget.cxx b/Qt/Components/pqDataInformationWidget.cxx +index f151d584fc8b683b5666c11c7dfad85219c1e94f..7079507a14bad98dd10bff7ddf65af896cf5e919 100644 +--- a/Qt/Components/pqDataInformationWidget.cxx ++++ b/Qt/Components/pqDataInformationWidget.cxx +@@ -103,8 +103,8 @@ pqDataInformationWidget::pqDataInformationWidget(QWidget* _parent /*=0*/) + this->Model->setActiveView(pqActiveObjects::instance().activeView()); + + // Clicking on the header should sort the column. +- QObject::connect(this->View->horizontalHeader(), SIGNAL(sectionClicked(int)), this->View, +- SLOT(sortByColumn(int))); ++ QObject::connect(this->View->horizontalHeader(), &QHeaderView::sectionClicked, this->View, ++ [=](int col) { this->View->sortByColumn(col, Qt::AscendingOrder); }); + + // Set the context menu policy for the header. + this->View->horizontalHeader()->setContextMenuPolicy(Qt::CustomContextMenu); +diff --git a/Qt/Components/pqDisplayRepresentationWidget.cxx b/Qt/Components/pqDisplayRepresentationWidget.cxx +index 3e08e05e560618457e628afc9bf1fdbf3167b9f0..4d9bc9958a0034e3e2b1e7920a333a5d7f794db6 100644 +--- a/Qt/Components/pqDisplayRepresentationWidget.cxx ++++ b/Qt/Components/pqDisplayRepresentationWidget.cxx +@@ -111,8 +111,8 @@ pqDisplayRepresentationWidget::pqDisplayRepresentationWidget(QWidget* _p) + { + this->Internal = new pqDisplayRepresentationWidget::pqInternals(); + this->Internal->setupUi(this); +- this->connect(this->Internal->comboBox, SIGNAL(currentIndexChanged(const QString&)), +- SLOT(comboBoxChanged(const QString&))); ++ QObject::connect(this->Internal->comboBox, &QComboBox::currentTextChanged, this, ++ &pqDisplayRepresentationWidget::comboBoxChanged); + } + + //----------------------------------------------------------------------------- +diff --git a/Qt/Components/pqLinksEditor.cxx b/Qt/Components/pqLinksEditor.cxx +index 6f02d16d44b82f616a236557f16174d3ffa96425..ae66b1c97c3d82425c2f8b849c6d656deecc64a8 100644 +--- a/Qt/Components/pqLinksEditor.cxx ++++ b/Qt/Components/pqLinksEditor.cxx +@@ -452,8 +452,8 @@ pqLinksEditor::pqLinksEditor(vtkSMLink* link, QWidget* p) + QObject::connect(this->Ui->lineEdit, SIGNAL(textChanged(const QString&)), this, + SLOT(updateEnabledState()), Qt::QueuedConnection); + +- QObject::connect(this->Ui->comboBox, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(updateSelectedProxies()), Qt::QueuedConnection); ++ QObject::connect(this->Ui->comboBox, &QComboBox::currentTextChanged, this, ++ &pqLinksEditor::updateSelectedProxies, Qt::QueuedConnection); + + QObject::connect( + this->Ui->interactiveViewLinkCheckBox, &QCheckBox::stateChanged, this, +diff --git a/Qt/Core/pqFileDialog.cxx b/Qt/Core/pqFileDialog.cxx +index 2a87c723a5ef4af856c71e3589ce9a5efa95b65b..6f369d1163a32e5ae3c7e3bcc00a22081e81e2a2 100644 +--- a/Qt/Core/pqFileDialog.cxx ++++ b/Qt/Core/pqFileDialog.cxx +@@ -322,7 +322,7 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.NavigateForward, SIGNAL(clicked(bool)), this, SLOT(onNavigateForward())); + impl.Ui.NavigateUp->setIcon(style()->standardPixmap(QStyle::SP_FileDialogToParent)); +- impl.Ui.NavigateUp->setShortcut(Qt::ALT + Qt::Key_Up); ++ impl.Ui.NavigateUp->setShortcut(Qt::ALT | Qt::Key_Up); + impl.Ui.NavigateUp->setToolTip( + tr("Navigate Up (%1)").arg(impl.Ui.NavigateUp->shortcut().toString())); + impl.Ui.CreateFolder->setIcon(style()->standardPixmap(QStyle::SP_FileDialogNewFolder)); +@@ -378,8 +378,8 @@ pqFileDialog::pqFileDialog(pqServer* server, QWidget* p, const QString& title, + QObject::connect( + impl.Ui.Parents, SIGNAL(activated(const QString&)), this, SLOT(onNavigate(const QString&))); + +- QObject::connect(impl.Ui.EntityType, SIGNAL(currentIndexChanged(const QString&)), this, +- SLOT(onFilterChange(const QString&))); ++ QObject::connect( ++ impl.Ui.EntityType, &QComboBox::currentTextChanged, this, &pqFileDialog::onFilterChange); + + QObject::connect(impl.Ui.Favorites, SIGNAL(clicked(const QModelIndex&)), this, + SLOT(onClickedFavorite(const QModelIndex&))); +diff --git a/Qt/Widgets/pqSignalAdaptors.cxx b/Qt/Widgets/pqSignalAdaptors.cxx +index 0015c9148b80eddd926ba37c17b7d777250c1a78..8e218b945c5f7a8962ffaced17d4a011c00db153 100644 +--- a/Qt/Widgets/pqSignalAdaptors.cxx ++++ b/Qt/Widgets/pqSignalAdaptors.cxx +@@ -16,10 +16,15 @@ + pqSignalAdaptorComboBox::pqSignalAdaptorComboBox(QComboBox* p) + : QObject(p) + { +- QObject::connect(p, SIGNAL(currentIndexChanged(const QString&)), this, +- SIGNAL(currentTextChanged(const QString&))); +- +- QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SIGNAL(currentIndexChanged(int))); ++ QObject::connect( ++ p, &QComboBox::currentTextChanged, this, &pqSignalAdaptorComboBox::currentTextChanged); ++ ++#if QT_VERSION > QT_VERSION_CHECK(6, 0, 0) ++ QObject::connect( ++ p, &QComboBox::currentIndexChanged, this, &pqSignalAdaptorComboBox::currentIndexChanged); ++#else ++ QObject::connect(p, SIGNAL(currentIndexChanged(int)), this, SLOT(currentIndexChanged(int))); ++#endif + } + + //---------------------------------------------------------------------------- diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 3921d7fefac..1c02282d891 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1767,17 +1767,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'runtest': False, # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.45', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9f4f7abbc69ea58ab7f24992d47f7391bb4aed6fb701fedaeb1a9f1cdc7fab8a'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 9754ce8b0ae..35ab629e89e 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1770,16 +1770,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb index 39679dc0366..cee5ad02ae6 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.2-GCCcore-13.3.0.eb @@ -1776,16 +1776,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), - ('Time::HiRes', '1.9764', { - 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], - }), ('Term::ReadLine::Gnu', '1.46', { 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.70', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 87d1215a591..944e2124f79 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1505,6 +1505,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.62', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index ec2e80d1840..497e05a273d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1610,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 11d6a08c241..54c05db3b92 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1603,6 +1603,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 2b37316b16c..3a6727d62a4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1610,6 +1610,8 @@ exts_list = [ 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], + # make sure that library provided by ncurses dependency is used instead of libtermcap + 'preinstallopts': "sed -s 's/-ltermcap/-lncurses/g' Makefile.PL && ", }), ('ExtUtils::MakeMaker', '7.64', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e752171a582 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '10.4.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8c7c3c0fc2952ff11b9a8c60365e098ee5334427dd5688c3584e77c25a7e1b3f'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +use_pip = True +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..34c086c859a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.4.0-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.4.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['166c1cd4d24309b30d61f79f4a9114b7b2313d7450912277855ff5dfd7cd4a06'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2'), + ('libwebp', '1.4.0'), + ('OpenJPEG', '2.5.2'), + ('LittleCMS', '2.16'), +] + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb new file mode 100644 index 00000000000..a0e995d4f45 --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.2.0-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Platypus-Opt' +version = '1.2.0' + +homepage = 'https://github.com/Project-Platypus/Platypus' +description = """Platypus is a framework for evolutionary computing in Python with a focus on + multiobjective evolutionary algorithms (MOEAs).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7150de2e24f8003c911259c575493c9351a7dcfb132445a3f3b096728634e6a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'platypus'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9b4c1f62855 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.4-GCCcore-13.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2e17a90062403e15d6540480fdec50c8b005eb48729a91cb4989ffeb04df193c'] + +builddependencies = [ + ('binutils', '2.42'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.3.1'), + ('OpenSSL', '3', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb index 258c21fef24..db7151ab47f 100644 --- a/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/ProteinMPNN/ProteinMPNN-1.0.1-20230627-foss-2022a-CUDA-11.7.0.eb @@ -27,17 +27,20 @@ dependencies = [ ('torchaudio', '0.12.0', '-PyTorch-1.12.0' + versionsuffix), ] -postinstallcmds = ['chmod a+x %(installdir)s/protein_mpnn_run.py'] +postinstallcmds = [ + 'chmod a+x %(installdir)s/protein_mpnn_run.py', + 'chmod a+x %(installdir)s/helper_scripts/*.py' +] sanity_check_paths = { 'files': ['protein_mpnn_run.py'], 'dirs': ['examples'], } -fix_python_shebang_for = ['protein_mpnn_run.py'] +fix_python_shebang_for = ['protein_mpnn_run.py', 'helper_scripts/*.py'] sanity_check_commands = ['protein_mpnn_run.py --help'] -modextrapaths = {'PATH': ''} +modextrapaths = {'PATH': ['', 'helper_scripts']} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb index aee9ba9ea19..894b488cd3e 100644 --- a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.8.7-GCCcore-12.3.0.eb @@ -43,6 +43,7 @@ exts_list = [ ('ansys-pythonnet', '3.1.0rc3', { 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], 'modulename': 'pythonnet', + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', }), ('pytomlpp', '1.0.13', { 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], diff --git a/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb new file mode 100644 index 00000000000..f2436367baa --- /dev/null +++ b/easybuild/easyconfigs/p/PyAEDT/PyAEDT-0.9.9-gfbf-2023b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'PyAEDT' +version = '0.9.9' + +homepage = 'https://aedt.docs.pyansys.com/version/stable' +description = """PyAEDT is a Python library that interacts directly with the +Ansys Electronics Desktop (AEDT) API, enabling straightforward and efficient +automation in your workflow.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('dotNET-Core', '8.0', '', SYSTEM), + ('libspatialindex', '1.9.3'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('Pillow', '10.2.0'), + ('pydantic', '2.6.4'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('dotnetcore2', '3.1.23', { + 'sources': ['dotnetcore2-3.1.23-py3-none-manylinux1_x86_64.whl'], + 'checksums': ['5f076ddc39da0c685e7de20ecb91ee81185928918ec86fbeb3bffc55dd867ab5'], + }), + ('clr_loader', '0.2.6', { + 'checksums': ['019348ae6b6a83c7a406d14537c277cecf7a3a53b263ec342c81ded5845a67ee'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('fonttools', '4.53.1', { + 'modulename': 'fontTools', + 'checksums': ['e128778a8e9bc11159ce5447f76766cefbd876f44bd79aff030287254e4752c4'], + }), + ('ansys-pythonnet', '3.1.0rc3', { + 'modulename': 'pythonnet', + 'checksums': ['369a0a5a838a0991f755b6d63c319ab6997f9dc464d016187227be5cd860a9cb'], + 'preinstallopts': 'export OPENSSL_ENABLE_SHA1_SIGNATURES=1 &&', + }), + ('pytomlpp', '1.0.13', { + 'checksums': ['a0bd639a8f624d1bdf5b3ea94363ca23dbfef38ab7b5b9348881a84afab434ad'], + }), + ('fpdf2', '2.7.9', { + 'modulename': 'fpdf', + 'checksums': ['f364c0d816a5e364eeeda9761cf5c961bae8c946f080cf87fed7f38ab773b318'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('rpyc', '6.0.0', { + 'checksums': ['a7e12b31f40978cbd6b74e0b713da389d4b2565cef612adcb0f4b41aeb188230'], + }), + ('rtree', '1.3.0', { + 'modulename': 'rtree', + 'checksums': ['b36e9dd2dc60ffe3d02e367242d2c26f7281b00e1aaf0c39590442edaaadd916'], + }), + ('pyedb', '0.21.0', { + 'checksums': ['3c91cb8a72a080864d3582ae7ec1de2f04d90aee477dadc096a7144f7823258d'], + }), + ('pyaedt', version, { + 'checksums': ['714728230ab3ede4744a30a7c0d45aaa104cdc1887bfbfe8feb928a8f10cc72f'], + }), +] + +modloadmsg = "NOTE: You also need load a AEDT module before you start using PyAEDT." + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb new file mode 100644 index 00000000000..47fce7ec459 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBullet/PyBullet-3.2.6-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'PyBullet' +version = '3.2.6' + +homepage = 'https://github.com/bulletphysics/bullet3' +description = """Bullet Physics SDK: real-time collision detection and +multi-physics simulation for VR, games, visual effects, robotics, +machine learning etc.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pybullet', version, { + 'checksums': ['da27525433c88698dc9fd8bc20fa4ae4d07738b4656633659ebd82c2d2884e08'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb new file mode 100644 index 00000000000..37d00512c27 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2024.1.6.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2024.1.6" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['539961408de4217a68b84d666d5c10ddb8d7bcf919e3a569f2489438a3237f1a'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb index ee4425b49c5..96d813edcce 100644 --- a/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyClone/PyClone-2020.9b2-GCCcore-10.2.0.eb @@ -21,9 +21,8 @@ dependencies = [ ('Python', '3.8.6'), ] -exts_default_options = { - 'use_pip': True -} +sanity_pip_check = True +use_pip = True exts_list = [ ('Logbook', '1.5.3', { @@ -37,6 +36,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb new file mode 100644 index 00000000000..5769add932d --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-384-gompi-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-384' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python310.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['630108f2bac166563fd2a4046a1d82e51e14693bb0e20dd3174e71c02b0760c2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb new file mode 100644 index 00000000000..f68a1a2ba06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.7.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.7.0' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b47250e5bb853e37db5db423bafc82847f4cde0ffdf7aebb06336a993bc174f6'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy + ('meson-python', '0.13.2'), + ('Cython', '3.0.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..50b9ad427e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.2-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0.2' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['https://github.com/yaml/pyyaml/archive/refs/tags/%(version)s.tar.gz'] +checksums = ['9377c381ac3fccad8df73d96b5139ef8b1a2c57a0d913e95ab0a2275d66b5caa'] + +builddependencies = [ + ('binutils', '2.42'), + ('Cython', '3.0.10'), +] +dependencies = [ + ('Python', '3.12.3'), + ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2024.06'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..54edd0b830e --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.18.0' + +homepage = 'https://pygments.org/' +description = """Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications + that need to prettify source code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_PY3_WHL] +checksums = ['b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': [], +} + +sanity_check_commands = ['pygmentize --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 6a91bcca5e4..808285d9f26 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.23.1'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-06-26 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index d551945f5e7..d97f7a93c0f 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -26,11 +26,8 @@ dependencies = [ ('virtualenv', '20.24.6'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2023-10-29 diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb index add89b7ae32..42df4fd52a1 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2024.06-GCCcore-13.3.0.eb @@ -28,11 +28,8 @@ dependencies = [ ('virtualenv', '20.26.2'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True # order is important! # package versions updated 2024-06-14 @@ -56,9 +53,6 @@ exts_list = [ ('pbr', '6.0.0', { 'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'], }), - ('Cython', '3.0.10', { - 'checksums': ['dcc96739331fb854dcf503f94607576cfe8488066c61ca50dfd55836f132de99'], - }), ('six', '1.16.0', { 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], }), diff --git a/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..92658cc24b7 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20240722-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20240722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c7335471f776af28bea9464ad85a50f2ed120f78fbf75ead6647aeea8e0e53f0'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Perl', '5.38.2')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb new file mode 100644 index 00000000000..a944c674694 --- /dev/null +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.17.4-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'petsc4py' +version = '3.17.4' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['216c3da074557946615d37d0826bc89f1f2e599323e2dacbdc45326d78bd50c6'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PETSc', version), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from petsc4py import PETSc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..bc9d066a13d --- /dev/null +++ b/easybuild/easyconfigs/p/phasius/phasius-0.2.0-GCC-12.3.0.eb @@ -0,0 +1,393 @@ +easyblock = 'Cargo' + +name = 'phasius' +version = '0.2.0' + +homepage = 'https://github.com/wdecoster/phasius' +description = """A tool to visualize phase block structure from (many) BAM, + CRAM or VCF files together with BED annotation""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wdecoster/phasius/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.2.0.tar.gz': 'a5b320303383b473661fccf7ec93f3b555b21d86d78d9cdaf5317cc9bcf3cb0e'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'android-tzdata-0.1.1.tar.gz': 'e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0'}, + {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'}, + {'anstream-0.6.15.tar.gz': '64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'anstyle-parse-0.2.5.tar.gz': 'eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb'}, + {'anstyle-query-1.1.1.tar.gz': '6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a'}, + {'anstyle-wincon-3.0.4.tar.gz': '5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8'}, + {'askama-0.12.1.tar.gz': 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'9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] + +crates = [ + ('aho-corasick', '1.1.3'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('anstream', '0.6.15'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.5'), + ('anstyle-query', '1.1.1'), + ('anstyle-wincon', '3.0.4'), + ('askama', '0.12.1'), + ('askama_derive', '0.12.5'), + ('askama_escape', '0.10.3'), + ('askama_parser', '0.2.1'), + ('atty', '0.2.14'), + ('autocfg', '1.3.0'), + ('base64', '0.13.1'), + ('basic-toml', '0.1.9'), + ('bindgen', '0.69.4'), + ('bio-types', '1.0.4'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.1.15'), + ('cexpr', '0.6.0'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.38'), + ('clang-sys', '1.8.1'), + ('clap', '3.2.25'), + ('clap_derive', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('colorchoice', '1.0.2'), + ('core-foundation-sys', '0.8.7'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('ctor', '0.2.8'), + ('curl-sys', '0.4.74+curl-8.9.0'), + ('custom_derive', '0.1.7'), + ('darling', '0.20.10'), + ('darling_core', '0.20.10'), + ('darling_macro', '0.20.10'), + ('deranged', '0.3.11'), + ('derive-new', '0.5.9'), + ('derive-new', '0.6.0'), + ('dyn-clone', '1.0.17'), + ('either', '1.13.0'), + ('env_filter', '0.1.2'), + ('env_logger', '0.11.5'), + ('erased-serde', '0.4.5'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.2.1'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.2.15'), + ('glob', '0.3.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('hex', '0.4.3'), + ('hts-sys', '2.1.4'), + ('humansize', '2.1.3'), + ('humantime', '2.1.0'), + ('iana-time-zone', '0.1.60'), + ('iana-time-zone-haiku', '0.1.2'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('ieee754', '0.2.6'), + ('indexmap', '1.9.3'), + ('is_terminal_polyfill', '1.70.1'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('lazycell', '1.3.0'), + ('libc', '0.2.158'), + ('libloading', '0.8.5'), + ('libm', '0.2.8'), + ('libz-sys', '1.1.20'), + ('linear-map', '1.2.0'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.5'), + ('minimal-lexical', '0.2.1'), + ('newtype_derive', '0.1.6'), + ('nom', '7.1.3'), + ('num-conv', '0.1.0'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('openssl-src', '300.3.1+3.3.1'), + ('openssl-sys', '0.9.103'), + ('os_str_bytes', '6.6.1'), + ('percent-encoding', '2.3.1'), + ('pkg-config', '0.3.30'), + ('plotly', '0.9.0'), + ('plotly_derive', '0.9.0'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.86'), + ('quick-error', '1.2.3'), + ('quote', '1.0.37'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rust-htslib', '0.47.0'), + ('rustc-hash', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustversion', '1.0.17'), + ('ryu', '1.0.18'), + ('semver', '0.1.20'), + ('serde', '1.0.209'), + ('serde_derive', '1.0.209'), + ('serde_json', '1.0.127'), + ('serde_repr', '0.1.19'), + ('serde_with', '2.3.3'), + ('serde_with_macros', '2.3.3'), + ('shlex', '1.3.0'), + ('strsim', '0.10.0'), + ('strsim', '0.11.1'), + ('strum_macros', '0.26.4'), + ('syn', '1.0.109'), + ('syn', '2.0.76'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('thiserror', '1.0.63'), + ('thiserror-impl', '1.0.63'), + ('time', '0.3.36'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.18'), + ('tinyvec', '1.8.0'), + ('tinyvec_macros', '0.1.1'), + ('typeid', '1.0.2'), + ('unicase', '2.7.0'), + ('unicode-bidi', '0.3.15'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.23'), + ('unzip-n', '0.1.2'), + ('url', '2.5.2'), + ('utf8parse', '0.2.2'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.5'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + +builddependencies = [ + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), + ('Clang', '16.0.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b15cf9f2ef6 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.43.4-GCCcore-13.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'pixman' +version = '0.43.4' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0624db90180c7ddb79fc7a9151093dc37c646d8c38d3f232f767cf64b85a226'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb new file mode 100644 index 00000000000..f66c2f13358 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.3.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('pkgconf', '2.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fcf1a67d7ff --- /dev/null +++ b/easybuild/easyconfigs/p/plotly-orca/plotly-orca-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'Binary' + +name = 'plotly-orca' +version = '1.3.1' + +homepage = 'https://github.com/plotly/orca' +description = """Orca is an Electron app that generates images and reports of Plotly things like + plotly.js graphs, dash apps, dashboards from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/plotly/orca/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['25ebf207d75769c140dcea033a984e7a3a6d919bb8e110a14c890c8cf430f14d'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/orca'], + 'dirs': ['lib/node_modules/orca'], +} +sanity_check_commands = ['orca --help'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..4a188f7473b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-6.0-GCC-13.3.0.eb @@ -0,0 +1,48 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '6.0' + +homepage = 'http://portablecl.org' +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + 'de9710223fc1855f833dbbf42ea2681e06aa8ec0464f0201104dc80a74dfd1f2', # v6.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Clang', '18.1.8'), + ('hwloc', '2.10.0'), + ('libtool', '2.4.7'), + ('libxml2', '2.12.7'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb new file mode 100644 index 00000000000..9db2243c96e --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10-foss-2023a.eb @@ -0,0 +1,110 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.3.10' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.3.10_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.3.10.tar.gz': 'eb177018b310e508f7ad6b5d486cc29166404dd5f82879d0c26aceaff51d3768'}, + {'pod5-file-format-0.3.10_dep_fix.patch': '20dc87ab82d4b52ff7fb769d17c2478daf95f787b2a184c9d985e33e03038e31'}, +] + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Arrow', '14.0.1'), + ('SciPy-bundle', '2023.07'), + ('zstd', '1.5.5'), + ('flatbuffers', '23.5.26'), + ('pybind11', '2.11.1'), + ('Boost', '1.82.0'), + ('build', '1.0.3'), + ('HDF5', '1.14.0'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('polars', '0.20.2'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +# unpin polars and h5py versions in pod5 +local_preinstallopts = ( + "sed -i" + " -e 's/polars~=0.19/polars/'" + " -e 's/h5py~=3.10.0/h5py/'" + " pyproject.toml && " +) + +exts_list = [ + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + ('pod5', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['f2dcb1938fcf51c725393345e480c1d12711089d542a27446fb92fbe2e18ae60'], + }), +] + +# create POD5Version.cmake +# python -m setuptools_scm && python -m pod5_make_version shows wrong version +local_ver_sub_minor = version.split('.')[2] +preconfigopts = ( + 'cd %%(builddir)s/%%(name)s-%%(version)s/cmake && ' + 'touch POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MAJOR %%(version_major)s)">POD5Version.cmake && ' + 'echo "set(POD5_VERSION_MINOR %%(version_minor)s)">>POD5Version.cmake && ' + 'echo "set(POD5_VERSION_REV %s)">>POD5Version.cmake && ' + 'echo "set(POD5_NUMERIC_VERSION %%(version)s)">>POD5Version.cmake && ' + 'echo "set(POD5_FULL_VERSION %%(version)s)">>POD5Version.cmake && ' % local_ver_sub_minor +) + +# delete add_subdirectory(third_party/pybind11) from CMakeLists.txt +preconfigopts += "cd %(builddir)s/%(name)s-%(version)s && sed -i '/add_subdirectory(third_party/d' CMakeLists.txt && " +preconfigopts += 'cd %(builddir)s/easybuild_obj && ' + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib" -DZSTD_INCLUDE_DIR="$EBROOTZSTD/include"' + +# install lib_pod5 from wheel - dependency of pod5 +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch new file mode 100644 index 00000000000..a053f870ebe --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.3.10_dep_fix.patch @@ -0,0 +1,32 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) +diff -u c++/CMakeLists.txt.orig c++/CMakeLists.txt +--- c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -3,7 +3,7 @@ + if (ENABLE_CONAN) + find_package(Arrow REQUIRED CONFIG) + find_package(Boost REQUIRED CONFIG) +- find_package(Flatbuffers REQUIRED CONFIG) ++ find_package(FlatBuffers REQUIRED CONFIG) + find_package(zstd REQUIRED CONFIG) + find_package(ZLIB REQUIRED CONFIG) + +@@ -17,7 +17,7 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) + find_package(ZLIB REQUIRED) + +@@ -27,6 +27,7 @@ + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE diff --git a/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..91b5c7c74ba --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.19-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = '1.19' + +homepage = 'https://github.com/rpm-software-management/popt' +description = 'Popt is a C library for parsing command line parameters.' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['http://ftp.rpm.org/popt/releases/popt-1.x'] +sources = [SOURCE_TAR_GZ] +checksums = ['c25a4838fc8e4c1c8aacb8bd620edb3084a3d63bf8987fdad3ca2758c63240f9'] + +builddependencies = [ + ('binutils', '2.42') +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', ('lib/libpopt.a', 'lib64/libpopt.a'), ('lib/libpopt.so', 'lib64/libpopt.so')], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7a8779a9412 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ef58228ef61 --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-24.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '24.7.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['5d0fdf9e681036fb263a783d0298fc3af580a6e2a6cf1a3314ffc48dc3d91ccb'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..556cc0f1507 --- /dev/null +++ b/easybuild/easyconfigs/p/primecount/primecount-7.14-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'primecount' +version = '7.14' + +homepage = 'https://github.com/kimwalisch/primecount' +description = """primecount is a command-line program and C/C++ library that counts the number of primes ≤ x + (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/kimwalisch/primecount/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d867ac18cc52c0f7014682169988a76f39e4cd56f8ce78fb56e064499b1d66bb'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/primecount', 'include/primecount.h'] + + ['lib/libprimecount.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +sanity_check_commands = ["primecount -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..11244361d59 --- /dev/null +++ b/easybuild/easyconfigs/p/primecountpy/primecountpy-0.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'primecountpy' +version = '0.1.0' + +homepage = 'https://pypi.org/project/primecountpy' +description = "This is a Cython interface to the C++ library primecount." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Cython', '3.0.10'), + ('cysignals', '1.11.4'), + ('primecount', '7.14'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dfcdad173d1 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8cbde894708 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ed4aac1448e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-5.28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '5.28.0' + +homepage = 'https://github.com/google/protobuf/' +description = "Python Protocol Buffers runtime library." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['dde74af0fa774fa98892209992295adbfb91da3fa98c8f67a88afe8f5a349add'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('protobuf', version[2:]), # Major version is only used for the Python bindings +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'google.protobuf'} + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b5f959fc06b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-28.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '28.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'protocolbuffers' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['13e7749c30bc24af6ee93e092422f9dc08491c7097efa69461f88eb5f61805ce'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] +dependencies = [ + ('Abseil', '20240722.0'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c0aab8a54e --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psycopg' +version = '3.2.1' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a1071f66e07 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.4.4' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d39e368e0cd --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '2.0.0' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +exts_list = [ + (name, version, { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb new file mode 100644 index 00000000000..127a798d38a --- /dev/null +++ b/easybuild/easyconfigs/p/pyfasta/pyfasta-0.5.2-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +local_preinstallopts = ( + "sed -i" + " -e 's/from fasta/from pyfasta.fasta/'" + " -e 's/from records/from pyfasta.records/'" + " -e 's/from split_fasta/from pyfasta.split_fasta/'" + " %(name)s/__init__.py && " +) +local_preinstallopts += "sed -i 's/from collections/from collections.abc/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/from records/from pyfasta.records/' pyfasta/fasta.py && " +local_preinstallopts += "sed -i 's/import cPickle/import _pickle as cPickle/' pyfasta/records.py && " +local_preinstallopts += "sed -i 's/from cStringIO import StringIO/from io import StringIO/' pyfasta/split_fasta.py && " + +exts_list = [ + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['pyfasta extract --help'] +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb new file mode 100644 index 00000000000..16cf7b1a00c --- /dev/null +++ b/easybuild/easyconfigs/p/pyseer/pyseer-1.3.12-foss-2023a.eb @@ -0,0 +1,56 @@ +# Borrowed from the BEAR RSG team, University of Birmingham +# Update: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'pyseer' +version = '1.3.12' + +homepage = 'https://github.com/mgalardini/pyseer' +description = """pyseer was first written a python reimplementation of seer, which was written in C++. pyseer uses + linear models with fixed or mixed effects to estimate the effect of genetic variation in a bacterial population + on a phenotype of interest, while accounting for potentially very strong confounding population structure. + This allows for genome-wide association studies (GWAS) to be performed in clonal organisms + such as bacteria and viruses.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pybedtools', '0.9.1'), + ('statsmodels', '0.14.1'), + ('scikit-learn', '1.3.1'), + ('Pysam', '0.22.0'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('glmnet-python', '1.0.2', { + 'source_urls': ['https://github.com/johnlees/glmnet_python/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7a5550514140dabbd27ad4eb1c04db64199d9bb89541e088d9bb162570205e76'], + }), + (name, version, { + 'source_urls': ['https://github.com/mgalardini/pyseer/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aa07fc1bd5346d02123ff36ba64a1ff4dbbb85a21c37a12f35ad7d5be7e21e9c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyseer', 'bin/square_mash'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + '%(namelower)s --help', + 'square_mash --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..7a512df4e25 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = "Runs tests multiple times to expose flakiness." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..25aaab957da --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'pytest-workflow' +version = '2.1.0' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), + ('python-isal', '1.7.0'), + ('zlib-ng', '2.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zstandard', '0.23.0', {'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09']}), + ('xopen', '2.0.2', {'checksums': ['f19d83de470f5a81725df0140180ec71d198311a1d7dad48f5467b4ad5df6154']}), + (name, version, {'checksums': ['dc86ad9a5f94482aec14926788f6b78b428be68ee0428cbca22f89b6326f8b7a']}), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb index 9d0b6f0c25d..45ab5fae484 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -13,11 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), + ('flit', '3.9.0'), ] dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), + ('hypothesis', '6.82.0'), ] use_pip = True @@ -39,15 +40,14 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('setuptools-scm', '8.0.4', { - 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], }), - ('flit-core', '3.9.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', - 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + ('exceptiongroup', '1.1.1', { + 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], }), - ('hypothesis', '6.88.1', { - 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], }), ('elementpath', '4.1.5', { 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb index 01e1aa2d9c6..3b61ec3f869 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -20,6 +20,7 @@ dependencies = [ ('Clang', '16.0.4'), ('libxml2', '2.10.3'), ('zlib', '1.2.12'), + ('cairo', '1.17.4'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..96885969511 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.7.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.7.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] +dependencies = [ + ('Python', '3.12.3'), + ('ISA-L', '2.31.0'), +] + +source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')] +sources = ['isal-%(version)s.tar.gz'] +checksums = ['9eb9457ed27fd0a8a7b403a5f4f9e6c8d1a44c2ca28ecd2f2bf3aed90b0a74bf'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb new file mode 100644 index 00000000000..5c6085a41e6 --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] + +dependencies = [ + ('Python', '3.10.8'), + ('networkx', '3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..400fecee609 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f208a034542 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.3.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + {'qwt-6.3.0.tar.bz2': 'dcb085896c28aaec5518cbc08c0ee2b4e60ada7ac929d82639f6189851a6129a'}, + {'Qwt-6.2.0_fix-install-prefix.patch': 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Qt5', '5.15.10'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..0c20434dec2 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023a.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb new file mode 100644 index 00000000000..347b09bccf3 --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2023b.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.11.5'), + ('Biopython', '1.84'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb new file mode 100644 index 00000000000..99c6ebe1e23 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('numba', '0.58.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 48c86d2ed02..7d2ebad2d77 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1352,6 +1352,15 @@ exts_list = [ ('plyranges', '1.22.0', { 'checksums': ['fcdcad1082fadd1a365dd2d2cc7d955601b737ecd4a567d888d2b445756297fc'], }), + ('seqPattern', '1.34.0', { + 'checksums': ['6037d3685bab94e2d1f6046bdc19369a786a595ef421e6ce7d8a34408a6f4967'], + }), + ('genomation', '1.34.0', { + 'checksums': ['6c7e40caee1115a28617c2a0a0837c92701dbce7511277c078a5957a50e877ed'], + }), + ('ChIPseeker', '1.38.0', { + 'checksums': ['a0d4710fccda620b750f933916acac6d12999a077e1c17632d8823848a2fa82f'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index bbc343accac..972a8488f6a 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -867,7 +867,10 @@ exts_list = [ 'checksums': ['8e50415e415702402473caf622d86b89ddc881f6e5d888079a4818a8807ac9a2'], }), ('bold', '1.3.0', { - 'checksums': ['0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f'], + 'checksums': [ + ('0ead11d4386c4c0cd578d3a956f809db2001e387e449a431b4ad503f3da38f5f', + '4920fbebd22fb1d0f1a31ccc09c98aec446bb6cb5f65a2610437e405c0512c68'), + ], }), ('rredlist', '0.7.1', { 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], @@ -3424,6 +3427,9 @@ exts_list = [ ('rhandsontable', '0.3.8', { 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb new file mode 100644 index 00000000000..0ff705e9788 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb @@ -0,0 +1,3463 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2024.06' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Xvfb', '21.1.9'), + ('Autotools', '20220317'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('R', '4.4.1'), + ('libxml2', '2.11.5'), # for XML + ('GMP', '6.3.0'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '74.1'), # for rJava & gdsfmt + ('HDF5', '1.14.3'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-34'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '20.9.0'), # for V8 (required by rstan) + ('GDAL', '3.9.0'), # for sf + ('MPFR', '4.2.1'), # for Rmpfr + ('PostgreSQL', '16.1'), # for RPostgreSQL +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.20', { + 'checksums': ['3ffe06a0685123c36cd306b874f89a59a70c864c8f78c5569f82a86abedc21db'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.12', { + 'checksums': ['08af355a9a10fe29d48d085abc7cf1f975e1a4a670668a4f8d9632d087fb41bf'], + }), + ('bnlearn', '4.9.4', { + 'checksums': ['ce3d8d89451fed9277f879c03bb02bc17acab13f1f35587aab8175b80246eeea'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.5', { + 'checksums': ['dee9b6c1152db1a5dc427d074b32bbbb738708683f17a95e0e95e4d79fdf174b'], + }), + ('gdata', '3.0.0', { + 'checksums': ['a456b9921765a705fe8e51780dfbbc6ca005abc948b2f80effeccd468601b17f'], + }), + ('GSA', '1.03.3', { + 'checksums': ['5459786190f40339addc45e7bb58c6a983548aa8feac7277ea7ec0662c5a282c'], + }), + ('infotheo', '1.2.0.1', { + 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], + }), + ('lars', '1.3', { + 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], + }), + ('lazy', '1.2-18', { + 'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'], + }), + ('kernlab', '0.9-32', { + 'checksums': ['654ef34e343deb4d2c4c139a44e5397d6e38876088ce1c53c7deb087935d6fdc'], + }), + ('markdown', '1.13', { + 'checksums': ['385421c674cf5bf2ba04d1df7c16bb5d857bec03755a36321999ac37f5b3cfd9'], + }), + ('mlbench', '2.1-5', { + 'checksums': ['4dbfd652adda7c0caf544d3a6cd23a2ee97c22faefe4d15b8a6782061cc9e76f'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '6.1.1', { + 'checksums': ['ddd7018e5e6ea7f92c7fc9872b391491b7e91c2cd89ef1dcaf4408afb5116775'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-61', { + 'checksums': ['3144c8bf579dd7b7c47c259728c27f53f53e294e7ed307da434dfd144e800a90'], + }), + ('lattice', '0.22-6', { + 'checksums': ['4b377211e472ece7872b9d6759f9b9c660b09594500462eb6146312a1d4d00f7'], + }), + ('nlme', '3.1-165', { + 'checksums': ['fc37bba493c2138be2f38fcfd2a67327d81ab91a37bad6f698226bb400ec9499'], + }), + ('segmented', '2.1-0', { + 'checksums': ['6d7ba0248cb5aa23dfdfc3fc53b6aab2f564323c671420fc73c5274e03640cf2'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.7', { + 'checksums': ['6b5527e2635c0ff762eb7af8154704c85e66d7f79a9524089a5c98dfa94dab08'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3.1', { + 'checksums': ['8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c'], + }), + ('pspline', '1.0-20', { + 'checksums': ['eaa7cd9b870d5d10cf457c435ebcbe698ba0d463e3a996fbe758a4b57b93eb8a'], + }), + ('timeDate', '4032.109', { + 'checksums': ['402841bda47e8c31f49773de2ff5447e9780bc7c8af5fb18be9287b546fcb958'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('pixmap', '0.4-13', { + 'checksums': ['e3dbc641a0497575b45a4140dadc6bf43cdf39b02393f93f1b0ee4f4d026e711'], + }), + ('sp', '2.1-4', { + 'checksums': ['e185e7fb61d2d7dbc50fd765a93e170fa778083a653588db1f5e99d019479f0a'], + }), + ('hms', '1.1.3', { + 'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'], + }), + ('progress', '1.2.3', { + 'checksums': ['ea2b079b894de85c3ab12088c9c52aec06432245047a961d5b4b8aa6889f9276'], + }), + ('RcppArmadillo', '0.12.8.4.0', { + 'checksums': ['cabf6865073204c184ddad4dec1f30aae1b8020b4c9d6e74d1a6b0baaef03046'], + }), + ('ade4', '1.7-22', { + 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], + }), + ('AlgDesign', '1.2.1', { + 'checksums': ['5989626c526bd7c3d9bdda326c962056879be03392065a0b7ddb9b8cf9309d05'], + }), + ('BH', '1.84.0-0', { + 'checksums': ['6fb660755f572cd975073d7052075654acf8db12d208954ca223b8e4f77ef1ac'], + }), + ('Matrix', '1.7-0', { + 'checksums': ['fb97bba0df370222eb4f7e2da2e94dd01053b5e054b1c51829ff9a6efc08ad37'], + }), + ('Brobdingnag', '1.2-9', { + 'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'], + }), + ('corpcor', '1.6.10', { + 'checksums': ['71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09'], + }), + ('longitudinal', '1.1.13', { + 'checksums': ['57f04a0f387c1cc30d2feb945dc3ed35d2a304d94d21d3bc2cac8c92571fdc10'], + }), + ('backports', '1.5.0', { + 'checksums': ['0d3ed9db8f1505e88967f48d669b2a257e0c6b7e6320ea64b946c1bd40897ca2'], + }), + ('checkmate', '2.3.1', { + 'checksums': ['e7e6ba0cca400137f352a599ea29cf35a83f40a5ad26e7c4f06e6c35471884f6'], + }), + ('cubature', '2.1.0', { + 'checksums': ['5d82785609611200d5bea069b93b0bf75bafec808f7eeef7b052eb516f273665'], + }), + ('DEoptimR', '1.1-3', { + 'checksums': ['8dd8a61b07b02022493d7021dc62ef2c4dc2d596cff897846713c5f8dd784694'], + }), + ('fastmatch', '1.1-4', { + 'checksums': ['9a914cac9c1ea2984bd44eebe421e1636504907a8064ae26347fe3ec2b9bd56b'], + }), + ('iterators', '1.0.14', { + 'checksums': ['cef3075a0930e1408c764e4da56bbadd4f7d14315809df8f38dd51f80ccc677b'], + }), + ('maps', '3.4.2', { + 'checksums': ['53e57b889f1779cfd4a116a8ed3eded7ed29a73a1b9506248772a389c8404b0c'], + }), + ('nnls', '1.5', { + 'checksums': ['cd70feb286f86f6dead75da693a8f67c9bd3b91eb738e6e6ac659e3b8c7a3452'], + }), + ('sendmailR', '1.4-0', { + 'checksums': ['5b8b91fc13f6b07b9fc5a2cf7591cf760fad47c5ea17d87a2891898c506454ad'], + }), + ('dotCall64', '1.1-1', { + 'checksums': ['21b8d7d747c07aaf8a82d61ec98fe0539afcaa5a565d9c2fc55be65b6af2c91b'], + }), + ('spam', '2.10-0', { + 'checksums': ['719c86a23801ecf051ffd8291912ee3567af4010e74af470fbf09e274728ac79'], + }), + ('subplex', '1.8', { + 'checksums': ['3bc31d8990380c9f790c9c7d84cb2e39f4945eff934eddfa1196d597465be5a5'], + }), + ('logspline', '2.1.22', { + 'checksums': ['773af7a2f12bce0eac30a036bd61bafd9a2b0eb083e377f4ef4e5518a463ed02'], + }), + ('ncbit', '2013.03.29.1', { + 'checksums': ['847f570c035d849e775c1cb922d2775e6c535971eb4429cf62904319fd126504'], + }), + ('permute', '0.9-7', { + 'checksums': ['eff88ffb579aaeb994e9f8609b776b2d9d9d56bc2879ddf180e3a2ad19f48dc0'], + }), + ('plotrix', '3.8-4', { + 'checksums': ['e6a22d93ab61c67af21cbbe1fe333c06934cf576a44745bf2beee59bceaae8d6'], + }), + ('randomForest', '4.7-1.1', { + 'checksums': ['f59ea87534480edbcd6baf53d7ec57e8c69f4532c2d2528eacfd48924efa2cd6'], + }), + ('scatterplot3d', '0.3-44', { + 'checksums': 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('RcppEigen', '0.3.4.0.0', { + 'checksums': ['28d4a02011129f9b7a2a2bbe69ec4cca7676b072d5aca9dc1cefa8f96af45136'], + }), + ('interp', '1.1-6', { + 'checksums': ['3674044e5334ecdf124054303929c084fc0797d3123e28576a230492ea6ecd34'], + }), + ('latticeExtra', '0.6-30', { + 'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'], + }), + ('plyr', '1.8.9', { + 'checksums': ['15b5e7f711d53bf41b8687923983b8ef424563aa2f74c5195feb5b1df1aee103'], + }), + ('gtable', '0.3.5', { + 'checksums': ['b19fc1a30359945adbab7d4e915fe95523a839c380e34ae705d70b7ebddeea72'], + }), + ('reshape2', '1.4.4', { + 'checksums': ['d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8'], + }), + ('dichromat', '2.0-0.1', { + 'checksums': ['a10578e9ad8a581bd8fe0d8a8370051f3cdcf12c7d282f3af2a18dacda566081'], + }), + ('colorspace', '2.1-0', { + 'checksums': ['04078abb6b54119c90dc7085d62916bf292ccb163e213f9ea70567d1be82614c'], + }), + ('munsell', '0.5.1', { + 'checksums': 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['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-8', { + 'checksums': ['6a06440d4b58e8a7f122747d92046ff40da4bb58a20bf642228a648a0c826ea7'], + }), + ('MCMCpack', '1.7-0', { + 'checksums': ['846073d710017ec1dc9a2b4616cb6aeb60ce04e3500a37214522818d34045def'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.44.0.3', { + 'checksums': ['61a85f6c2f15e8e96839f8a4fd3a45eaa6bca90517bb20a4dd36e951d6fd0c82'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.14', { + 'checksums': ['66e455bb0e66d3c04af84d9dddc9b89f40b4cf9fe9ad1cf0714bcf30aa1b6837'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-8', { + 'checksums': ['2c2049c7cb868a2e4e1a530fe7218fac56e6157ef64ad57b91c5bb457dbc9821'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-13', { + 'checksums': ['7e5d312fca8029d746f60e7d9e701129561942f97dfc33b036b123f159d69a4c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.1.1', { + 'checksums': ['8c2448f176ed94201affb8a9c42a5d0f56f26e88131ff2c1f4a9d14c5a0d87f6'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-7', { + 'checksums': ['c3505e5ac06d5e01b3a6bad94177f8375cd9867bb0146cc9c63d92424ecb7922'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.2', { + 'checksums': ['6051b07019003c698ae016d79f13945bfe2edec26f8a688126b978cb90adcfff'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.2-1', { + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], + }), + ('sampling', '2.10', { + 'checksums': ['fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775'], + }), + ('lda', '1.5.2', { + 'checksums': ['95d354786e002352a973052df993b9d3acfc9f9598a053afb95ac27c7e150fd4'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.2', { + 'checksums': ['3354b22752f0aa0c0d9c8c12b38810202b6380f2587e539be11d9a358412fe6a'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25.1', { + 'checksums': ['d92a0cf819fe4c08b8eb17f5e03275c8accde7f3b54f990cbba5ab926575b60b'], + }), + ('emdbook', '1.3.13', { + 'checksums': ['26044b7ea1b42304b4dfde48afa94dd487acf979da4db2bf670ba41222083c19'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.6', { + 'checksums': ['61bd0d19d045b50c6764f3a7c95ce1e734af9e5f964449825d002afe02109489'], + }), + ('tictoc', '1.2.1', { + 'checksums': ['8fcdb7c9a1e4b4817bcab654effd64dea6ec749a7901d4060d5b5c625fc88833'], + }), + ('ISOcodes', '2024.02.12', { + 'checksums': ['02cb7b918034085dffcba0d329a2bc52514873f898a3a716560ebf17b57ae2e6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], + }), + ('SnowballC', '0.7.1', { + 'checksums': ['753cf13f3206751662c03b1cf39bce9e680024f6d9f8503b836a83797181c034'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], + }), + ('hunspell', '3.0.3', { + 'checksums': ['fdaa1473a62dff2a5923b9bd958d87e546069ca22ce113f44e88c761338442f3'], + }), + ('topicmodels', '0.2-16', { + 'checksums': ['0d5c9c65dd7ba031ba81adc0984d3e36b0309ada2204644bf816370ae656e905'], + }), + ('tidytext', '0.4.2', { + 'checksums': ['0cf4180c2ab9fdb158337a7bfb6ba32f15fb61aae28abce425deaa5933ed2d54'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.3-1', { + 'checksums': ['216a1a5bb18c7a7dfb13c6c162228c6c81c45408f04d7784b6e60ae6cd4745d2'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.4', { + 'checksums': ['bb944389a61cff22bb3bdde938a0ff6c16700a1ca725ef36b391b97812c45b26'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('distributional', '0.4.0', { + 'checksums': ['09b5f3279bed4c79575f75d5f7f5e3e593c7838434a78c89f0b7184e8f20e602'], + }), + ('posterior', '1.5.0', { + 'checksums': ['4a10307fcae321f2cd4ca7871504a0c6c9152b8473dc9a033721e8dcda18e2de'], + }), + ('loo', '2.7.0', { + 'checksums': ['7664f331555e569d6037100048681e3a696fb9ca2e87907712eb54faa85bcb36'], + }), + ('RcppParallel', '5.1.7', { + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], + }), + ('StanHeaders', '2.32.9', { + 'checksums': ['27b0feb34e1200193e3a31a951d28c5adc91c93dc0454732545b8078132e0b33'], + }), + ('V8', '4.4.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['e7bc35f3420f5f537121d681a90c16a74b36dc17210c9425e7f03842493a9670'], + }), + ('QuickJSR', '1.2.2', { + 'checksums': ['51842f846585c8dfdab155eb5a26be0735cae280fa1c1bff1907d718525968ed'], + }), + ('rstan', '2.32.6', { + 'checksums': ['3390d00191bbd3b0739dd19fe437b99a041a6b04be208877b48419d1348a1a70'], + }), + ('Rborist', '0.3-7', { + 'checksums': ['011efef9e6f304f752bd5013627dc8482f0e9d4cf1ec49503e97d3718f542596'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], + }), + ('mRMRe', '2.1.2.1', { + 'checksums': ['d53c392e82a437005b71d0e8b97350d0237608fffafe087700fe7f6770167fd9'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '3.2.0', { + 'checksums': ['41d8ed4c01c3740028bdf2ba9c5550f1142061e4a40c93b1d2160719c59c3c4a'], + }), + ('ggsignif', '0.6.4', { + 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.2', { + 'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.6.0', { + 'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'], + }), + ('yaImpute', '1.0-34', { + 'checksums': ['b4c898c95fca784480bbbc239c78c85dc9f45a96c34c563ea7e81248ef8a8a73'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('leiden', '0.4.3.1', { + 'checksums': ['a9ecbbcfa2724d8fdd0133af569278e036b25b6e2cbb23d453092cc6b3fc30e2'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('packrat', '0.9.2', { + 'checksums': ['69df5943257e6c4d06f3d907241b668b53dedece72158ca935260b8b8e1672d7'], + }), + ('colourpicker', '1.3.0', { + 'checksums': ['c7f2618cd1ae1f7ac15aee072c648e6494dfff6714e13dc7cd1da993d1102510'], + }), + ('ggExtra', '0.10.1', { + 'checksums': ['6879edfe8e3905a2c299cbd18777422223ad30042bc6e20614ca5109a75de82c'], + }), + ('findpython', '1.0.8', { + 'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'], + }), + ('argparse', '2.2.3', { + 'checksums': ['a50cc4e1221f063e472a8cfe7e881a1d4abed5ef93cf40d5f65a2528cdfd2674'], + }), + ('intergraph', '2.0-4', { + 'checksums': ['585f2f9fa92aa52022dfdcbe597a3654099ca63c1d4110a0f8e895fa32fc59c9'], + }), + ('ggnetwork', '0.5.13', { + 'checksums': ['6c297ead19dbd89de3278f3705410b757f2d9744bc466d8175105833a4e1fd46'], + }), + ('qqman', '0.1.9', { + 'checksums': ['3f6a931771d375174b78f220471ddd601def9b5c69631931b0992ebbc8c5bc13'], + }), + ('rstantools', '2.4.0', { + 'checksums': ['bff72ca2f0352c6c5d2868823e286fdb73a6ead74508a4124cbcb222c83b4faa'], + }), + ('bayesplot', '1.11.1', { + 'checksums': ['4f71e67391e0135acd3e890989b87025f3f8160242f532a8e1a0ed74ed0f3830'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('renv', '1.0.7', { + 'checksums': ['7b60b58a23743803ab167f82f78663e86f778947b2bda07afa12689338794507'], + }), + ('PKI', '0.1-14', { + 'checksums': ['c024e81977b978b705460df96639e3369420bd7e8f4f3242ec796255dc1b7966'], + }), + ('rsconnect', '1.3.1', { + 'checksums': ['47de8a832da493e2a1b3243fb42459a53eb193f75a1143348b7d8c7478cb5557'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2023-10.21', { + 'checksums': ['0d732d5604c26af59cfb95b80ed4e226c9c10422e2d82a6cc06b92f9ba6a44b5'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('memisc', '0.99.31.7', { + 'checksums': ['b403185850520db18ebd608df85c76df80e6c64af428cdc4e49c2fe487483637'], + }), + ('mclogit', '0.9.6', { + 'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'], + }), + ('projpred', '2.8.0', { + 'checksums': ['b383ddc5eca275737b96e4e3e14256b4f4abc4b29d292b5cebf3828d0921a1f6'], + }), + ('brms', '2.21.0', { + 'checksums': ['7289ff33c2a4b83584b7fece0a6aa53fd14b5881a467d417fbca5dbf62ec5d58'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.9.1', { + 'checksums': ['c2136a7a5b3a6b71c8ba3cdfc7e83c14b400c9197c1544f0967297659e3b8631'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.4.1', { + 'checksums': ['1c277248ad00122f404aabd0f0bbdeaf1cd69c58b65faaf23e36ee39f1e750c7'], + }), + ('maxlike', '0.1-11', { + 'checksums': ['6dde7bb4a46d5509a1fee024c2fd1d13c82e14a80806969ec89359103ade01e9'], + }), + ('coxme', '2.2-20', { + 'checksums': ['a0eeeadaabe81458b4fe80d26ca9770ff17dc3a2a41a37b2d1b09fadb887cb62'], + }), + ('AICcmodavg', '2.3-3', { + 'checksums': ['4055b5f1fc12917b9f812c056e6a2dbf23bbd0169e468f567306ddf29d699f7a'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.4.0', { + 'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.8.0', { + 'checksums': ['8b5cd096404291d39778ec4fed36cd25719fa0ca4225866e67566c4d346d2ce8'], + }), + ('rgdal', '1.6-7', { + 'checksums': ['555cedfdadb05db90b061d4b056f96d8b7010c00ea54bc6c1bbcc7684fadae33'], + }), + ('rgeos', '0.6-4', { + 'checksums': ['9d03c4de96fd3fad55ff8d1ff8113dcaaa00f15d9d0588e54c9f91751bcede11'], + }), + ('mapproj', '1.2.11', { + 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.4', { + 'checksums': ['b1826899f33640541752f2b68ed4d23530fe62744ac4714adf79ff748fc6701a'], + }), + ('ridigbio', '0.3.8', { + 'checksums': ['e518dbaeaf7f0dd0b833d83a6a094e07c5bd84935279c9e35bb69fe35ee00288'], + }), + ('spocc', '1.2.3', { + 'checksums': ['ee14de78a9a91bf4220b3317d724f9e4953fda8b5478b2083690c984903db951'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-6', { + 'checksums': ['385939708b6a3657663409f91e165ded0ff5268d1dc6225e0f9b34764baf2d2c'], + }), + ('fasterize', '1.0.5', { + 'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'], + }), + ('BIEN', '1.2.6', { + 'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'], + }), + ('rangeModelMetadata', '0.1.5', { + 'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], + }), + ('plotmo', '3.6.3', { + 'checksums': ['6917cd8185325f1f2998fb14def9e6a8d93f1b708cf70d7c443d3960c9189b7b'], + }), + ('earth', '5.3.3', { + 'checksums': ['786a0fcabb3db13e0e0a4ba61ecccb7e171030b39bc97926f8e7159485d2f572'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.7.1', { + 'checksums': ['f7912ccf3a583a27208f74ca15c3b272cc930bae6b10ae7e5958ff2951ee9723'], + }), + ('biomod2', '4.2-5-2', { + 'checksums': ['1c4ca427b8d6af54de548023dcbe25c7e9cbea7afb684c58b66f4210af9eb4e5'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-5', { + 'checksums': ['b27cb2795cb59592d474cfaf49a21657a8878404da4f01c556f7323e953b4c5b'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-28', { + 'checksums': ['d2e4b4ee1c191e7c506be3fec5a5e877c1b36754cba558bd75eaac9cc6ac0138'], + 'preinstallopts': local_dbarts_preinstallopts, + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('minty', '0.0.1', { + 'checksums': ['cfbdc6603c8fb54ea4d43091e2aee4c99212e6e20a335ed89576156d86237acd'], + }), + ('readODS', '2.3.0', { + 'checksums': ['1e120ff8fdb34c7e00f07726b4843cfaeee9c680bfdc2982e83422c24e4c0491'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': 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['ff3d8e4ec7764333144d461eb5ea7a4adbf5b5f29f84c3ec3e60a93802e2f5bb'], + }), + ('CVXR', '1.0-13', { + 'checksums': ['81895c750a562d04bb6840ef7744f3a2dd6232b076d5c18ecdcf30a60f83875a'], + }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), + ('officer', '0.6.6', { + 'checksums': ['f1fc3f7a9299da1fd09864da4ae6b8c47c6491f0119da86863b1c9470caeb412'], + }), + ('gfonts', '0.2.0', { + 'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'], + }), + ('fontBitstreamVera', '0.1.1', { + 'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'], + }), + ('fontLiberation', '0.1.0', { + 'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'], + }), + ('fontquiver', '0.2.1', { + 'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'], + }), + ('gdtools', '0.3.7', { + 'checksums': ['d292c3b8574adc38007662085c3d1cf5d17e8019f085295d594380d85cf2b394'], + }), + ('flextable', '0.9.6', { + 'checksums': ['232e050bec231b5d58ca8ad54116c476d2dd683ac2824b3688c06250338f9229'], + }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), + ('ggdist', '3.3.2', { + 'checksums': ['f6563091cb7ca48b4fb415740a60113be6aac541616f5025110364e12cbe83f1'], + }), + ('svUnit', '1.0.6', { + 'checksums': ['263e6c03d6c2717dfd25b96d25f8019c9c98120de280a17224e0d79adba2d522'], + }), + ('arrayhelpers', '1.1-0', { + 'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'], + }), + ('tidybayes', '3.0.6', { + 'checksums': ['706044e17855a684a5ad1aeb582963dd3c7192a4a8ad0584358d0ea7c7aadb90'], + }), + ('spdep', '1.3-5', { + 'checksums': ['ba8efa06ddbc12408f4f6d4c85606d84922131d9c05953e0b23b81f03e56e626'], + }), + ('stringmagic', '1.1.2', { + 'checksums': ['eed1c04aa99be5a99ecfdd32498279f170e261669cc1b91d18673454064b8f8c'], + }), + ('dreamerr', '1.4.0', { + 'checksums': ['3e5e4afd10623b6dac6bb9b8bf0480d41c7422884cfec2d9d9786414f9026a87'], + }), + ('fixest', '0.12.1', { + 'checksums': ['7ce71ab9856b17000aae7dd578b1b99a43fee35116500626005056b4d9e713df'], + }), + ('cmna', '1.0.5', { + 'checksums': ['7cf99880cb70e8fd0b022184167888b1ad32dca503e0250c1d552a84f0613898'], + }), + ('XBRL', '0.99.19.1', { + 'checksums': ['ad9ebb5431bdfecc38b8bf3b2552f1a048878a9ac02f5a9d71279b3b099a9757'], + }), + ('rhandsontable', '0.3.8', { + 'checksums': ['901ed9c59936f7fa52ad8db3111c8904ab962f9c74f1b6cd40f81683af35d21d'], + }), + ('missMDA', '1.19', { + 'checksums': ['f9675884829b2fef75237c335b21991d163674320e766523c71c7a853f95e65c'], + }), + ('insight', '0.20.3', { + 'checksums': ['b60e189849cd3c368e9c2b2174e89c2dfbba3b34e84feb8a20af1bb758116bb2'], + }), + ('datawizard', '0.12.2', { + 'checksums': ['fee36520440131596394878eb19f295609ef5d7997a3a5614c059f2a8d2be081'], + }), + ('bayestestR', '0.14.0', { + 'checksums': ['fa0f94204b414df05ecf7340b37fbb5fbe6dff2d057e2425a6990b6510054880'], + }), + ('performance', '0.12.2', { + 'checksums': ['b55e663eb45b8e88625c704506f20c4068a1c892c5a6a94d7bd0c0e3a7ed4028'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb new file mode 100644 index 00000000000..4981b999b95 --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.2.1-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.2.1' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('R', '4.3.2'), + ('poppler', '23.09.0'), + ('tesseract', '5.3.4'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('qpdf', '1.3.3', { + 'checksums': ['415610be6fa73f60a31872b81fea089288b07f9cb6d078088009207c5e60fe53'], + }), + ('pdftools', '3.4.0', { + 'checksums': ['0b9d7b2100a6d7959c56e144285b9638ca6ff4a7f484a31ff814a99d71482c64'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['ffaba641c5d531a2b6d4ded3608a669206b1e0690cb5e013e3fc9db8aea117fe'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['qpdf', 'pdftools'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8b9d1c97fe..9d09c819514 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -57,6 +57,10 @@ dependencies = [ osdependencies = [OS_PKG_OPENSSL_DEV] +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + configopts = "--with-pic --enable-threads --enable-R-shlib" # some recommended packages may fail in a parallel build (e.g. Matrix), and # we're installing them anyway below diff --git a/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb new file mode 100644 index 00000000000..09a46feeaa1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.4.1-gfbf-2023b.eb @@ -0,0 +1,371 @@ +name = 'R' +version = '4.4.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 24 June 2024 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.4', { + 'checksums': ['f2d74527508bf3287102470beb27de0d234c3cbba399c28d3312f2c83c64a6e1'], + }), + ('Rcpp', '1.0.12', { + 'checksums': ['0c7359cc43beee02761aa3df2baccede1182d29d28c9cd49964b609305062bd0'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.3', { + 'checksums': ['4295085f11221c54b1dd2b1d39a675a85dfd9f900294297567e1d36f65ac4841'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.4', { + 'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'], + }), + ('xfun', '0.45', { + 'checksums': ['3816f05c2fd297b40750be1a2f386f0aa4637136421f504d14b6ad9ea0993611'], + }), + ('commonmark', '1.9.1', { + 'checksums': ['9517a13f4ce4a99bb157493453b04419b222cb65a9471cd3b11e5045ac0db53b'], + }), + ('highr', '0.11', { + 'checksums': ['e90d14284001963325a84a9dbeef029609d52515da8d65c87ae61be21b7fe0a7'], + }), + ('digest', '0.6.36', { + 'checksums': ['d1777364b2358b3ff9d79428fa7c1b280042f88896302765b0d0e2d4dc7ae637'], + }), + ('desc', '1.4.3', { + 'checksums': ['54468da73dd78fc9e7c565c41cfe3331802c2134b2e61a9ad197215317092f26'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.2.0', { + 'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'], + }), + ('crayon', '1.5.3', { + 'checksums': ['3e74a0685541efb5ea763b92cfd5c859df71c46b0605967a0b5dbb7326e9da69'], + }), + ('stringi', '1.8.4', { + 'checksums': ['c219f8f64d1a2bfd4ca9528452d44d30db1899af14f4b9ef248412443bc669f3'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('evaluate', '0.24.0', { + 'checksums': ['e23d764a58e7525257d57da4ccfee9d6f63b5b3c18bf01c76818ec8c9c587fd6'], + }), + ('ps', '1.7.6', { + 'checksums': ['52c35ffc3d1e1d984a94c7bbd671ef4ad70946990cbcd80e814e17937b056dd2'], + }), + ('processx', '3.8.4', { + 'checksums': ['6627672d7fb109f37dc1d0eaef913f4cfc7ad8ac807abf0397e6d37753b1e70b'], + }), + ('callr', '3.7.6', { + 'checksums': 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['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'], + }), + ('lifecycle', '1.0.4', { + 'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'], + }), + ('vctrs', '0.6.5', { + 'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'], + }), + ('stringr', '1.5.1', { + 'checksums': ['a4adec51bb3f04214b1d8ef40d3a58949f21b1497cbeaf2ba552e0891eef45de'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], + }), + ('testthat', '3.2.1.1', { + 'checksums': ['d785ce3975939e28b61048b0e28d881c80904534ff21e5b1a79a0a934124e9f7'], + }), + ('xml2', '1.3.6', { + 'checksums': ['e81991ff99bff3616dde8683c1327194e3ea64fa3b8062f52d8ce32673dd308f'], + }), + ('curl', '5.2.1', { + 'checksums': ['4a7a4d8c08aa1bca2fcd9c58ade7b4b0ea2ed9076d0521071be29baac8adfa90'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], + }), + ('openssl', '2.2.0', { + 'checksums': ['18b8b46ae8db4bd57c7bcc8e10d0bb549ae63e383502051cef86102ab617ddb3'], + }), + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.9', { + 'checksums': ['e133049aad7964e0f6150257e1470b3748f36029322265ee797b8caf7517d4d2'], + }), + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], + }), + ('cachem', '1.1.0', { + 'checksums': ['550839fc2ae5d865db475ba2c1714144f07fa0c052c72135b0e4a70287492e21'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.7.0', { + 'checksums': ['2135d9841af382673b815a14454abff2f2ce0f5dc97484d1499298b85b752ca0'], + }), + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], + }), + ('tinytex', '0.51', { + 'checksums': ['bb113b51b4b58e78902a0220d709650c1458a8c6d3fa03f58ba007f0eb74c8ea'], + }), + ('rmarkdown', '2.27', { + 'checksums': ['61e9cb3eab4f8587fea98d3358652695b7e77eda858caa4c8985241ba6502b9f'], + }), + ('downlit', '0.4.4', { + 'checksums': ['55c377dcee4adc48c1060e14079f3d1832453d066a2cf070530caa210c48f828'], + }), + ('cpp11', '0.4.7', { + 'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'], + }), + ('systemfonts', '1.1.0', { + 'checksums': ['1941069bd20320284ec026a38c53cb736be60bda431303ceaf8fd27ae13fb644'], + }), + ('textshaping', '0.4.0', { + 'checksums': ['35e940786bb278560de61bb55d4f46f8c86c878d0461613ceb8c98ba9b239d7a'], + }), + ('ragg', '1.3.2', { + 'checksums': ['8037a45209fdd50acf101208af8e832b840a11ad4201cf7fb480de432e6b6931'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.9', { + 'checksums': ['6e542216c03b5286cb9901175d1a7937a664db2572bc28bb51e9000269fcdda0'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.3.0', { + 'checksums': ['f8209df3bab33340c1bc8c0d26caee2890fafb93129ff1423302abae5931fad3'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.15', { + 'checksums': ['5e6ded3623a39df3e1db6cb7e7292b4c03c80b3c6c5faaac3b78b711cb205ed0'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.1.1', { + 'checksums': ['a38d5fb5d750e2c2091ce9101f138c1f9bc7009bbb195227a3519c5d97e36753'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.1', { + 'checksums': ['e3b278b8c324a1aa2650141dd89d01253eea5c2555007422c797915689b29aec'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.5.0', { + 'checksums': ['4d663f1426cd88d42f4070f23d969305c575e0499ed1397be6607b0770d2850c'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.1', { + 'checksums': ['33e92d830981b33cd5e55068b500c57dbfb72329c2fce54be3163c63b217f1b2'], + }), + ('gh', '1.4.1', { + 'checksums': ['76bd3f2a31eeaf76a633362899a20b0f7e8fb6159d4777baf3da2a47854292af'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4be8dccf690 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '7.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb new file mode 100644 index 00000000000..d218a83dc02 --- /dev/null +++ b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.11-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'RHEIA' +version = '1.1.11' + +homepage = 'https://github.com/rheia-framework/RHEIA' +description = "Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # deap, numpy, pandas, scipy + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), +] + +use_pip = True + +exts_list = [ + ('pvlib', '0.11.0', { + 'checksums': ['88b31c44dc07f0435af1e2d5ddcac067e6ce15917251a9f270366f61e9bd015b'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('SobolSequence', '0.2.1', { + 'modulename': 'sobol', + 'checksums': ['b2b4b57451b8d2e79ddb07efa23bc471dfdd436ea357d6368666bdc364df3eb1'], + }), + ('rheia', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['d6b1ea991f6338cca136b59e8e413bae2167c5ebd631163ec68fafe0040aa143'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb new file mode 100644 index 00000000000..22e6ed85f93 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.1-gompi-2023a.eb @@ -0,0 +1,65 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Update: Petr Král (INUITS) +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.14.1' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.14.1+-src.tar.gz': '712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'}, + {'isb-2.14.1+-rmblast.patch.gz': '9c8091eb2aec97ac83287859d2bfec83cb08c082d5a121cbefe3cc626f933763'}, +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost.MPI', '1.82.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LMDB', '0.9.31'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb new file mode 100644 index 00000000000..56585dad1c0 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2023.09.1+494-foss-2023a-Java-11-R-4.3.2.eb @@ -0,0 +1,108 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = "2023.09.1+494" +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = 'cd7011dce393115d3a7c3db799dda4b1c7e88711' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['38526a5816e980b12aeaef7debd2151f08ef2e54fed83af2622eb7cdeeb479a2'] + +builddependencies = [ + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('nodejs', '18.17.1'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%(start_dir)s/dependencies/common'", + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-panmirror", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + ' '.join([ + 'MYTMP=`mktemp -d`', + '&& export RSTUDIO_CONFIG_DIR="$MYTMP"', + '&& export XDG_DATA_HOME="$MYTMP/.data"', + '&& export XDG_CACHE_HOME="$MYTMP/.cache"', + '&& mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"', + '&& export RS_LOG_DIR="$MYTMP/log"', + '&& echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"', + '&& rserver', + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +modloadmsg = """ +The server can be started with: + rserver --server-daemonize=0 --www-port=8787 + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file="${MYTMP}/db.conf" +""" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..de4df21150d --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), + ('git', '2.42.0'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b296d76e7b7 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-20240815-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +# no new release since Aug'16 so using latest commit; +# see also https://github.com/Tencent/rapidjson/issues/2202 +version = '1.1.0-20240815' +local_commit = '7c73dd7' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'v%(version)s.tar.gz'}] +checksums = ['91138ebc9c980e554e6bcf9d13537f9eebf42710e0b956fdca46181ad645f94d'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-*/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..61c358020c8 --- /dev/null +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,55 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Based on Raptor2 RPM spec file: +# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec +# The RPM patches have been integrated in the version 2.0.16 +# +# Update: Petr Král (INUITS) +## +easyblock = 'ConfigureMake' + +name = 'Raptor' +version = '2.0.16' +homepage = 'https://librdf.org/raptor/' +description = """Set of parsers and serializers that generate Resource Description Framework +(RDF) triples by parsing syntaxes or serialize the triples into a syntax.""" +# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = ['raptor2-%(version)s.tar.gz'] +checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('make', '4.4.1'), +] + +dependencies = [ + ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), + ('cURL', '8.0.1'), + ('ICU', '73.2'), +] + +configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no" + +# fix error: 'xmlEntity' {aka 'struct _xmlEntity'} has no member named 'checked' +# see https://github.com/dajobe/raptor/pull/58 +local_sed_replacement = r's/LIBXML_VERSION >= 20627/LIBXML_VERSION >= 2062 \&\& LIBXML_VERSION < 21100/g' +prebuildopts = "sed -i '%s' src/raptor_libxml.c && " % local_sed_replacement + +sanity_check_paths = { + 'files': ['bin/rapper', 'lib/libraptor2.%s' % SHLIB_EXT], + 'dirs': ['include/raptor2/'] +} + +sanity_check_commands = ["rapper --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3d5e0ad9d83 --- /dev/null +++ b/easybuild/easyconfigs/r/Rasqal/Rasqal-0.9.33-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Rasqal' +version = '0.9.33' +homepage = 'hhttps://librdf.org/rasqal' +description = """A library handling RDF query syntaxes, construction and execution""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6924c9ac6570bd241a9669f83b467c728a322470bf34f4b2da4f69492ccfd97c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Raptor', '2.0.16'), +] + +dependencies = [ + ('libgcrypt', '1.10.3'), + ('MPFR', '4.2.0'), + ('PCRE', '8.45'), + ('gtk-doc', '1.34.0'), + ('ICU', '73.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-static --enable-release" + +sanity_check_paths = { + 'files': ['bin/roqet', 'lib/librasqal.%s' % SHLIB_EXT], + 'dirs': ['include/rasqal/'] +} + +sanity_check_commands = ["roqet --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9046d5c9362 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.0.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.3'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.4'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e2adb9db1d9 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-GCCcore-13.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('cURL', '8.3.0'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.11.5'), + ('libxslt', '1.1.38'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.11.5'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb new file mode 100644 index 00000000000..4e58793cd0a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2-Python-3.6.eb @@ -0,0 +1,95 @@ +# This EasyConfig is made with older setuptools and wheel versions, so that it still works with Python-3.6.X +# For newer python versions, we suggest to use ReFrame-4.6.2.eb (without suffix) +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' +versionsuffix = '-Python-3.6' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# Listed as python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +req_py_majver = 3 +req_py_minver = 6 + +# The setuptools in this EasyConfig is the latest that works for Python 3.6, but is too old for Python 3.12 +# See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269#discussion_r1741570244 +max_py_majver = 3 +max_py_minver = 11 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1, which is compatible with Python 3.6 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + # Require new enough setuptools to install with e.g. pyproject.toml + # 59.6.0 is the latest compatible with Python 3.6 + ('setuptools', '59.6.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + # stick to wheel 0.37.1, which is compatible with Python 3.6 + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb new file mode 100644 index 00000000000..26e331c131e --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.2.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +# Required by lxml, which is installed by ReFrame's bootstrap installer +osdependencies = [ + ('libxml2'), + ('libxslt', 'libxslt1.1'), +] + +# We use pip, setuptools and wheel compatible with Python 3.7 and above +# Note that ReFrame itself is compatible also with Python 3.6 +# As listed in the python_requires in https://github.com/reframe-hpc/reframe/blob/v4.6.2/setup.cfg +# To use with Python 3.6, please install ReFrame-4.6.2-Python-3.6.eb instead +req_py_majver = 3 +req_py_minver = 7 + +use_pip = True + +exts_list = [ + # stick to pip 24.0, which is compatible with Python 3.7 + # we still need pip outside of ReFrame's external dependencies, since the install cmd uses pip + ('pip', '24.0', { + 'use_pip': False, + 'checksums': ['ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2'], + }), + # Require new enough setuptools to work with Python 3.12, which doesn't have pkgutil.ImpImporter anymore + # See https://github.com/pypa/setuptools/commit/6653e747c3815b140156249205397ef3719581ee + # 68.0.0 is the latest compatible with Python 3.7 + ('setuptools', '68.0.0', { + 'use_pip': False, + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235'], + }), + # stick to wheel 0.42.0, which is compatible with Python 3.7 + ('wheel', '0.42.0', { + 'source_tmpl': 'wheel-%(version)s-py3-none-any.whl', + 'checksums': ['177f9c9b0d45c47873b619f5b650346d632cdc35fb5e4d25058e09c9e581433d'], + }), + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d3343815ee3d2c330b91a1cdb924ba184119ed7d9fc88a4a754b939a4259df82'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb new file mode 100644 index 00000000000..7217999a898 --- /dev/null +++ b/easybuild/easyconfigs/r/Redland/Redland-1.0.17-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Redland' +version = '1.0.17' + +homepage = 'https://librdf.org/raptor' +description = """Redland is a set of free software C libraries that + provide support for the Resource Description Framework (RDF).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['de1847f7b59021c16bdc72abb4d8e2d9187cd6124d69156f3326dd34ee043681'] + +dependencies = [ + ('Rasqal', '0.9.33'), + ('Raptor', '2.0.16'), + ('PostgreSQL', '16.1'), + ('MariaDB', '11.6.0'), + ('unixODBC', '2.3.12'), + ('SQLite', '3.42.0'), + ('libtool', '2.4.7'), +] + +sanity_check_paths = { + 'files': [ + 'include/%(namelower)s.h', + 'bin/%(namelower)s-config', + 'bin/%(namelower)s-db-upgrade', + 'lib/librdf.%s' % SHLIB_EXT, + ], + 'dirs': ['share/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..09b2ac462d6 --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/Regenie-3.1.2-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'MakeCp' + +name = 'Regenie' +version = '3.1.2' + +homepage = 'https://rgcgithub.github.io/regenie' +description = """Regenie is a C++ program for whole genome regression modelling of large genome-wide +association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/rgcgithub/regenie/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s_Makefile.patch'] +checksums = [ + 'b2e5e98bb310d9b9071ae5c63c5207be853bb1ec7918574e1acfdd0c83e744ff', # v3.1.2.tar.gz + '8be5d4b3b237d7a1820727061227857770554970aa136da614b71c14767e655e', # regenie-3.1.2_Makefile.patch +] + +dependencies = [ + ('Boost', '1.55.0'), + ('BGEN-enkre', '1.1.7'), + ('OpenBLAS', '0.3.18'), +] + +build_cmd = "make BGEN_PATH=$EBROOTBGENMINENKRE HAS_BOOST_IOSTREAM=1 " +build_cmd += "OPENBLAS_ROOT=$EBROOTOPENBLAS BOOST=$EBROOTBOOST STATIC=0" + +files_to_copy = [ + (['regenie'], 'bin'), + (['example/*'], 'example'), + (['docs/*'], 'docs'), +] + +sanity_check_commands = ['regenie --help'] + +sanity_check_paths = { + 'files': ['bin/regenie'], + 'dirs': ['bin', 'example', 'docs'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch new file mode 100644 index 00000000000..3fc4820cc4d --- /dev/null +++ b/easybuild/easyconfigs/r/Regenie/regenie-3.1.2_Makefile.patch @@ -0,0 +1,41 @@ +Patch to remove 3rd party software and replace lapack(e) with openblas and boost 1.55 +base on the work of Author: J. Sassmannshausen NHS/GSTT +diff -ruN regenie-3.1.1.orig/Makefile regenie-3.1.1/Makefile +--- regenie-3.1.1.orig/Makefile 2022-05-05 10:59:29.000000000 -0700 ++++ regenie-3.1.1/Makefile 2022-06-21 13:34:54.464076000 -0700 +@@ -44,7 +44,7 @@ + # detect OS architecture and add flags + UNAME_S := $(shell uname -s) + ifeq ($(UNAME_S),Linux) +- INC = -I${BGEN_PATH}/3rd_party/boost_1_55_0 ++ INC = -I${BOOST} + CFLAGS += -fopenmp + ifeq ($(strip $(STATIC)),1) + LPATHS = -static-libgcc -static-libstdc++ +@@ -103,10 +103,10 @@ + INC += -I${OPENBLAS_ROOT}/include/ + # static linking + ifeq ($(strip $(STATIC)),1) +- SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas + # dynamic linking + else +- DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas ++ DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -lopenblas -lgfortran + endif + endif + endif +@@ -119,11 +119,10 @@ + OBJECTS = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp)) + + PGEN_PATH = ./external_libs/pgenlib/ +-INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/ ++INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/include/ -I${BOOST}/include -I./external_libs/ + +-LPATHS += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/ + +-LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost ++LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost_system -lboost_filesystem -lboost_thread -lboost_timer + LIBS += -lz ${DLIBS} -lm -ldl -lgfortran + + diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb new file mode 100644 index 00000000000..90b43c163a0 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.7-p1-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.7-p1' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993'] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('TRF', '4.09.1'), + ('h5py', '3.9.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.4'), + ('RMBlast', '2.14.1'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..88962930f30 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.79.0-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.79.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.79.0-src.tar.gz': '172ecf3c7d1f9d9fb16cd2a628869782670416ded0129e524a86751f961448c0'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Python', '3.12.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '3', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b6fc9da5925 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.39')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b877029e19a --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.9-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.9' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), + ('Redis', '7.2.4'), +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c107fddbaa40414559ddd21f0a78bc7d466cd6b20a800839ac18b9bb54e5c150'], + }), +] + +sanity_pip_check = True + +moduleclass = "data" diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..f793f925da6 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-15-foss-2023a-R-4.3.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['35cd4c1faaaa8523b87ac053b881dccf29798f073f438459589e786b95ef18a1'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('JAGS', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..742dabcaa85 --- /dev/null +++ b/easybuild/easyconfigs/r/rnamotif/rnamotif-20240904-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'rnamotif' +version = '20240904' +_commit = '697ee7fda4ff2f5181a33c0c3eac54d7b97409fa' + +homepage = "https://github.com/dacase/rnamotif" +description = """The rnamotif program searchs input sequences for portions that match a given descriptor or "motif". + Matching sequences can also be ranked by various scoring functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'dacase' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['e9432e128ce7f1bfcf4898a36d56435272ad9b4e2d37f1866a95aa159c81fdfe'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + +] + +prebuildopts = 'sed -i "s/CFLAGS= -O2 -Wall/CFLAGS=$CFLAGS/" config.h &&' +pretestopts = 'EFNDATA=%%(builddir)s/%%(name)s-%s/efndata' % _commit +runtest = 'test' + +files_to_copy = [ + (['src/rnamotif', 'src/rmprune', 'src/rmfmt', 'src/rm2ct'], 'bin'), + 'LICENSE', 'efndata', 'Ecoli.trna.example', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['efndata'], +} + +sanity_check_commands = ['rnamotif -h 2>&1 | grep usage'] + +modextravars = {'EFNDATA': 'efndata'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..48d0b0d8bb5 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.18.6' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('poetry', '1.8.3'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.jinja2', '0.2.7', { + 'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + (name, version, { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb new file mode 100644 index 00000000000..2a86b64c9ae --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2023a.eb @@ -0,0 +1,170 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('Rust', '1.75.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + 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{'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb new file mode 100644 index 00000000000..796eb9a63b6 --- /dev/null +++ b/easybuild/easyconfigs/s/SCENICplus/SCENICplus-1.0a1-20240513-foss-2023a.eb @@ -0,0 +1,279 @@ +easyblock = 'PythonBundle' + +name = 'SCENICplus' +version = '1.0a1-20240513' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1'), + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), + ('Sphinx-RTD-Theme', '2.0.0'), + ('scrublet', '0.2.3'), + ('numexpr', '2.9.0'), + ('Kaleido', '0.2.1'), + ('pyfasta', '0.5.2'), + ('gensim', '4.3.2'), +] + +# fix requirements.txt of scenicplus +local_preinstallopts = ( + "sed -i" + " -e '/typing==3.7.4.3/d'" + " -e 's/==.*//g'" + " -e '/pyarrow-hotfix/d'" + " -e '/line-profiler/d'" + " -e '/ndindex/d'" + " -e '/sinfo/d'" + " requirements.txt && " +) +# unpin version restriction and delete typing requirement +local_pycistopic_preinstallopts = ( + "sed -i" + " -e 's/pyscenic>=0.12.0/pyscenic/'" + " -e 's/pandas==1.5/pandas/'" + " -e 's/python-Levenshtein/Levenshtein/'" + " -e 's/python-igraph/igraph/'" + " -e '/typing/d'" + # delete pyscenic and loomxpy req from commit - have versions now + " -e '/pyscenic@git/d'" + " -e '/loomxpy@git/d'" + " requirements.txt && " + "sed -i" + " -e 's/pandas == 1.5/pandas/'" + " -e 's/matplotlib < 3.7/matplotlib/'" + " pyproject.toml && " +) +# delete typing from requirements +local_pycistarget_preinstallopts = "sed -i '/typing/d' requirements.txt && " +# unpin version restriction and delete poetry.lock +local_loomxpy_preinstallopts = "sed -i 's/pyscenic>=0.12.0/pyscenic/' requirements.txt && " +local_loomxpy_preinstallopts += "sed -i 's/pyscenic = \">=0.12.0\"/pyscenic = \"*\"/' pyproject.toml && " +local_loomxpy_preinstallopts += "rm poetry.lock && " + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bs4', '0.0.2', { + 'checksums': ['a48685c58f50fe127722417bae83fe6badf500d54b55f7e39ffe43b798653925'], + }), + ('attr', '0.3.2', { + 'checksums': ['1ceebca768181cdcce9827611b1d728e592be5d293911539ea3d0b0bfa1146f4'], + }), + ('attrs', '23.2.0', { + 'checksums': ['935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30'], + }), + ('lda', '3.0.0', { + 'checksums': ['c9acbc1c55d2928f7e3e2336352b3382d78e43dbb0d12bf9ed97f87bce6d6708'], + }), + ('zope.interface', '6.2', { + 'checksums': ['3b6c62813c63c543a06394a636978b22dffa8c5410affc9331ce6cdb5bfa8565'], + }), + ('zope.event', '5.0', { + 'checksums': ['bac440d8d9891b4068e2b5a2c5e2c9765a9df762944bda6955f96bb9b91e67cd'], + }), + ('gevent', '24.2.1', { + 'checksums': ['432fc76f680acf7cf188c2ee0f5d3ab73b63c1f03114c7cd8a34cebbe5aa2056'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('suds-community', '1.1.2', { + 'modulename': 'suds', + 'checksums': ['883b4173ad23e7b20e9779ac7238b06140c50d7852afd5dc49dad1ea5f5a3d08'], + }), + ('grequests', '0.7.0', { + 'checksums': ['5c33f14268df5b8fa1107d8537815be6febbad6ec560524d6a404b7778cf6ba6'], + }), + ('pexpect', '4.9.0', { + 'checksums': ['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('easydev', '0.12.1', { + 'checksums': ['b47b7e6f75316ac9045b46487930e16ddb567f3899310deee11d72d8e1f0a231'], + }), + ('bioservices', '1.11.2', { + 'checksums': ['31baaab4ab813b93f79995ba8cad431a16cbee99e1b0c6f9e419dd4be0c73a9e'], + }), + ('gseapy', '0.10.8', { + 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pybigtools', '0.1.2', { + 'checksums': ['0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58'], + }), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('pyranges', '0.0.111', { + 'checksums': ['d2cf3c31c1b9c6e1bf6e1e89254d8bd993bfb4401f2c4ede0ebc9c8e0678147d'], + }), + ('pyrle', '0.0.39', { + 'checksums': ['1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5'], + }), + ('pyvis', '0.3.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5720c4ca8161dc5d9ab352015723abb7a8bb8fb443edeb07f7a322db34a97555'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests_cache', '1.2.0', { + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('scanorama', '1.7.4', { + 'checksums': ['67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + ('scatac_fragment_tools', '0.1.0', { + 'checksums': ['e77a03ad1b7170c212f1ac672dad2c5d7e7f091b94e47b36a2ec2adc42051857'], + }), + ('snakemake_interface_common', '1.17.1', { + 'checksums': ['555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae'], + }), + ('snakemake_interface_report_plugins', '1.0.0', { + 'checksums': ['02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('globre', '0.1.5', { + 'checksums': ['ee214204f237e9114b8f61eeb61c2abd1e665ca3b59e5a6a0b070971c0bb12e2'], + }), + ('bidict', '0.23.1', { + 'checksums': ['03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71'], + }), + ('tmtoolkit', '0.12.0', { + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('plumbum', '1.8.3', { + 'checksums': ['6092c85ab970b7a7a9d5d85c75200bc93be82b33c9bdf640ffa87d2d7c8709f0'], + }), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4', { + 'checksums': ['042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794'], + }), + ('nbsphinx-link', '1.3.0', { + 'checksums': ['fa3079a74c0dff1b2079e79a34babe770706ba8aa9cc0609c6dbfd593461a077'], + }), + ('numpydoc', '1.7.0', { + 'checksums': ['866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('ansicolors', '1.1.8', { + 'modulename': 'colors', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['00d2dde5a675579325902536738dd27e4fac1fd68f773fe36c21044eb559e187'], + }), + ('papermill', '2.6.0', { + 'checksums': ['9fe2a91912fd578f391b4cc8d6d105e73124dcd0cde2a43c3c4a1c77ac88ea24'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('marshmallow', '3.21.1', { + 'checksums': ['4e65e9e0d80fc9e609574b9983cf32579f305c718afb30d7233ab818571768c3'], + }), + ('dataclasses_json', '0.6.4', { + 'checksums': ['73696ebf24936560cca79a2430cbc4f3dd23ac7bf46ed17f38e5e5e7657a6377'], + }), + ('loomxpy', '0.4.2', { + 'preinstallopts': local_loomxpy_preinstallopts, + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '2.0a-dca4bb6', { + 'modulename': 'pycisTopic', + 'preinstallopts': local_pycistopic_preinstallopts, + # download commit dca4bb6 to be compatible with pycistarget + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'dca4bb6.tar.gz', 'filename': '%(name)s-%(version)s-dca4bb6.tar.gz'}], + 'checksums': ['82edc9313bbb587aeb1540fd5b095b6eafb422fa12a5fc97ba090b99b684b240'], + }), + ('pycistarget', '1.0a1-16d14b9', { + 'preinstallopts': local_pycistarget_preinstallopts, + # download commit 16d14b9 to make '$ scenicplus' work + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': '16d14b9.tar.gz', 'filename': '%(name)s-%(version)s-16d14b9.tar.gz'}], + 'checksums': ['7285ac03be9d148437442a726366d7c6f9f5f86bc6636369149a2bc2cd8e0e29'], + }), + ('scenicplus', version, { + 'preinstallopts': local_preinstallopts, + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['88cddec1ab2618861e5c93e8a0b17b8e9e2aa3a76410d882c35d472f98724e29'], + }), +] + +# copy files to let 'scenicplus init_snakemake' works +postinstallcmds = [ + "cp -r %%(builddir)s/scenicplus/scenicplus-%s*/src/scenicplus/snakemake " + "%%(installdir)s/lib/python%%(pyshortver)s/site-packages/scenicplus" % local_commit +] + +sanity_check_commands = ['scenicplus init_snakemake --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb new file mode 100644 index 00000000000..e7d07a0b329 --- /dev/null +++ b/easybuild/easyconfigs/s/SCRIPro/SCRIPro-1.0.18-foss-2023a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'SCRIPro' +version = '1.0.18' +local_commit = 'e9087fd' + +homepage = 'https://github.com/xuyunfan9991/SCRIPro' +description = "SCRIPro, an extended framework of SCRIP that suits both single-cell and spatial multi-ome data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('h5py', '3.9.0'), + ('scanpy', '1.9.8'), + ('Seaborn', '0.13.2'), + ('PyTables', '3.8.0'), + ('tqdm', '4.66.1'), + ('dill', '0.3.7'), + ('leidenalg', '0.10.2'), + ('PyTorch', '2.1.2'), + ('PyTorch-bundle', '2.1.2'), # provides PyTorch-Ignite + ('tensorboardX', '2.6.2.2'), + ('pybedtools', '0.9.1'), + ('jupyter-server', '2.7.2'), # ipywidgets +] + +use_pip = True + +exts_list = [ + ('lisa2', '2.3.2', { + 'checksums': ['dc9df3495322c94f93c12372fb8d88d355447f7b8b69ea639394fc6274e9affb'], + 'modulename': 'lisa', + }), + ('parse', '1.20.1', { + 'checksums': ['09002ca350ad42e76629995f71f7b518670bcf93548bdde3684fd55d2be51975'], + }), + ('pynvml', '11.5.0', { + 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + }), + ('sparse', '0.15.1', { + 'checksums': ['973adcb88a8db8e3d8047953331e26d3f64a5657f9b46a6b859c47663c3eef99'], + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", + }), + ('scglue', '0.3.2', { + 'checksums': ['fd57ebfa400233cbb1ab4fab4ad6a9dbf4db2c5ca715ba31c71c7a36cc931241'], + }), + ('scripro', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'source_urls': ['https://github.com/xuyunfan9991/SCRIPro/archive'], + 'sources': [{'download_filename': 'e9087fd.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6636c31f3f5797d33d57a5d0266c89f80cc37389dd9c139806b4d17ecad74252'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scripro'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scripro --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1c8130b397c --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.30.6-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.30.6' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6ef64ca18a19d13df6eb22df9aff19fb0db65610a74cc81dae33a82235cacd4'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('X11', '20240607'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb new file mode 100644 index 00000000000..9d2584de1bb --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb new file mode 100644 index 00000000000..5c7da32ecff --- /dev/null +++ b/easybuild/easyconfigs/s/SIRIUS/SIRIUS-7.5.2-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'SIRIUS' +version = '7.5.2' + +homepage = 'https://github.com/electronic-structure/SIRIUS' +description = """SIRIUS is a domain specific library for electronic structure calculations. +It implements pseudopotential plane wave (PP-PW) and +full potential linearized augmented plane wave (FP-LAPW) methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/electronic-structure/SIRIUS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9ae01935578532c84f1d0d673dbbcdd490e26be22efa6c4acf7129f9dc1a0c60'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxc', '6.2.2'), + ('HDF5', '1.14.0'), + ('spglib', '2.5.0'), + ('SpFFT', '1.1.0'), + ('spla', '1.6.1'), + ('COSTA', '2.2.2'), + ('Umpire', '2024.02.1'), +] + +sanity_check_paths = { + 'files': [ + 'bin/sirius.scf', + 'lib/libsirius.%s' % SHLIB_EXT, + ], + 'dirs': ['bin', 'include/sirius'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb new file mode 100644 index 00000000000..06a2de7582c --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-10.0.0-Java-11.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '10.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_linux-%(version)s.sh' +local_varfile = 'SNAP-ESA-8.0-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version_major)s_%(version_minor)s/installers', + 'https://step.esa.int/downloads/%(version_major_minor)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + {'esa-snap_all_linux-10.0.0.sh': 'c928fd886c983fa7c09c09a3c48593542e71b0636d493ae1401b4c964348698a'}, + {'SNAP-ESA-8.0-response.varfile': '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4'}, +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) +dependencies = [ + ('Java', '11'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['rstb', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --help | grep 'Additional module options'", + "gpt -h", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..e100da22edb --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('SQLite', '3.42.0'), + ('PostgreSQL', '16.1'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb index 42f094bb67b..a61fe5e85bb 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.1696'), +] + dependencies = [ ('HTSlib', '1.17'), ('zlib', '1.2.12'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb index 1943af96d5e..a017a2ba109 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb index cf16b5c2979..67cac5d0f47 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -24,6 +24,10 @@ checksums = [ {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, ] +builddependencies = [ + ('xxd', '9.0.2112'), +] + dependencies = [ ('HTSlib', '1.18'), ('zlib', '1.2.13'), @@ -31,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb index a86f215d8dd..886aa0a24c5 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-13.2.0.eb @@ -35,6 +35,9 @@ dependencies = [ start_dir = 'source' +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + buildopts = ' STAR && make STARlong' files_to_copy = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb new file mode 100644 index 00000000000..a0a119a428c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b_alpha_2024-02-09-GCC-12.3.0.eb @@ -0,0 +1,57 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11b_alpha_2024-02-09' + +homepage = 'https://github.com/dobinlab/STAR_pre_releases' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/dobinlab/STAR_pre_releases/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-2.7.11a_use-external-htslib.patch'] +checksums = [ + {'2.7.11b_alpha_2024-02-09.tar.gz': '7a7bae1f802fc5bc5b270da89e66a824480fb33e21f7ebfbf7ed56e1d4907c1c'}, + {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +builddependencies = [ + ('xxd', '9.0.2112'), +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +# by default this is set to -mavx2 which makes it fail on non x86 systems +prebuildopts = 'CXXFLAGS_SIMD= ' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb new file mode 100644 index 00000000000..dcc9d919c13 --- /dev/null +++ b/easybuild/easyconfigs/s/Sagemath/Sagemath-10.4-foss-2023b.eb @@ -0,0 +1,158 @@ +easyblock = 'PythonBundle' + +name = 'Sagemath' +version = '10.4' + +homepage = 'https://doc.sagemath.org/html/en/index.html' +description = """Sage is open source mathematical software released under the GNU General Public Licence GPLv2+, + and includes packages that have compatible software licenses. + People all around the globe have contributed to the development of Sage. Full documentation is available online.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('Cython', '3.0.10'), + ('Python-bundle-PyPI', '2023.10'), + ('Boost', '1.83.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('ECL', '24.5.10'), + ('FFLAS-FFPACK', '2.5.0'), + ('eclib', '20240408'), + ('GSL', '2.7'), + ('LinBox', '1.7.0'), + ('Singular', '4.4.0'), + ('libpng', '1.6.40'), + ('libgd', '2.3.3'), + ('m4ri', '20200125'), + ('cysignals', '1.11.4'), + ('gmpy2', '2.1.5'), + ('GMP-ECM', '7.0.5'), + ('MPFI', '1.5.4'), + ('cliquer', '1.21'), + ('nauty', '2.8.8'), + ('SYMMETRICA', '2.0'), + ('lcalc', '2.0.5'), + ('gap', '4.13.0'), + ('giac', '1.9.0-99'), + ('m4rie', '20200125'), + ('libhomfly', '1.02r6'), + ('libbraiding', '1.2'), + ('planarity', '3.0.2.0'), + ('rankwidth', '0.9'), + ('BRiAl', '1.2.12'), + ('bliss', '0.77'), + ('coxeter', '20180226'), + ('mcqd', '1.0.0'), + ('SharedMeatAxe', '1.0.1'), + ('sirocco', '2.1.0'), + ('tdlib', '0.9.3'), + ('pkgconfig', '1.5.5', '-python'), + ('matplotlib', '3.8.2'), + ('networkx', '3.2.1'), + ('sympy', '1.12'), + ('IPython', '8.17.2'), + ('Pillow', '10.2.0'), + ('fpylll', '0.6.1'), + ('primecountpy', '0.1.0'), + ('lrcalc', '2.1'), + ('PyZMQ', '25.1.2'), + ('tornado', '6.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cypari2', '2.2.0', { + 'checksums': ['817606bf661b71d33e1d012421907a4f8fb09dd81b7d3e3ae179b3978020bbf1'], + }), + ('memory_allocator', '0.1.4', { + 'checksums': ['d609216b03031967e2b45a804b12ff9029578f4ec019fde42cf6aed6ca09efe4'], + }), + ('sage_setup', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4797ceae2f5f636a756f4121011246445611f7a56bced2df431328fe013c52c7'], + }), + ('conway_polynomials', '0.10', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a354b4ac0a9985da75e2ac6ec6d7de2902396eff48913eeed86a962486171c28'], + }), + ('comm', '0.2.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3'], + }), + ('debugpy', '1.8.5', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55919dce65b471eff25901acf82d328bbd5b833526b6c1364bd5133754777a44'], + }), + ('nest_asyncio', '1.6.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c'], + }), + ('ipykernel', '6.29.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5'], + }), + ('jupyterlab_widgets', '3.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e3cda2c233ce144192f1e29914ad522b2f4c40e77214b0cc97377ca3d323db54'], + }), + ('widgetsnbextension', '4.0.13', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71'], + }), + ('ipywidgets', '8.1.5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245'], + }), + ('jupyter_core', '5.7.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409'], + }), + ('jupyter_client', '8.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f'], + }), + ('lrcalc', '2.1', { + 'checksums': ['e3a0509aeda487b412b391a52e817ca36b5c063a8305e09fd54d53259dd6aaa9'], + }), + ('%(namelower)s_standard', version, { + 'modulename': 'sage', + 'checksums': ['f6579e85f33bd9bb6e9b991bfc4c49dab1e649858ed9ee41c7cec75cb92d4c62'], + }), + ('%(namelower)s_bliss', version, { + 'modulename': False, + 'checksums': ['70cccef849908436c2f9f1aabb3992a21c90d3ce99d1a965743f0fdec3735d32'], + }), + ('%(namelower)s_coxeter3', version, { + 'modulename': False, + 'checksums': ['c4f20204b91a696caeb7ad7cf33d2b0398d26d287085b2cb9434e8b067716fca'], + }), + ('%(namelower)s_mcqd', version, { + 'modulename': False, + 'checksums': ['6a140d8b3866ea27aa5966f3aab86a882785862fb00ae37087beb09105b94175'], + }), + ('%(namelower)s_meataxe', version, { + 'modulename': False, + 'checksums': ['5b625333c3168fc2ab55d32ad7e8c41912858bde8010b5aadc70c6450fa967e8'], + }), + ('%(namelower)s_sirocco', version, { + 'modulename': False, + 'checksums': ['499304b3331751d7b0f62de8379afb073d55f144c5f73775da0c5b92160e3a7c'], + }), + ('%(namelower)s_tdlib', version, { + 'modulename': False, + 'checksums': ['018497a1e220d3320a37d1acb3eee59ec820d167c7916e95f0508709a2e31703'], + }), +] + +sanity_check_commands = [ + "sage --help", + "python -c 'from sage.all import *'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..9b52051eed3 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.3-GCC-12.3.0.eb @@ -0,0 +1,59 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +# # +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.10.3' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimate from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/COMBINE-lab/salmon/archive'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('jemalloc', '5.3.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] +dependencies = [ + ('Boost', '1.82.0'), + ('tbb', '2021.11.0'), + ('cURL', '8.0.1'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb new file mode 100644 index 00000000000..1bccc16f38b --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2024a-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.4.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb index b80b8631909..99d61098d6b 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024.05.eb @@ -16,7 +16,8 @@ builddependencies = [ ('Meson', '1.4.0'), ('meson-python', '0.16.0'), ('Ninja', '1.12.1'), - ('pkgconf', '2.2.0'), # required by scipy + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb new file mode 100644 index 00000000000..2abab977add --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -0,0 +1,103 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2024.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2024a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.103.1'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.4.0'), + ('meson-python', '0.16.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), # required by scipy + ('Cython', '3.0.10'), # required by numpy and scipy +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('pybind11', '2.12.0'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.26.4', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.26.4_fix-riscv64-test-failures.patch', + ], + 'checksums': [ + {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.26.4_fix-riscv64-test-failures.patch': + '81bd487dbca6da8285971a16a2c7b488718a051d3cd66450277bed6ff21741de'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.16.1', { + 'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.13.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + }), + ('numexpr', '2.10.0', { + 'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'], + 'checksums': [ + {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'}, + {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'}, + ], + }), + ('Bottleneck', '1.3.8', { + 'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'], + }), + ('tzdata', '2024.1', { + 'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'], + }), + ('pandas', '2.2.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.1', { + 'modulename': 'deap.base', + 'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb new file mode 100644 index 00000000000..9d7b53221e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a-CUDA-12.6.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb new file mode 100644 index 00000000000..eda406cbe2a --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2024a.eb @@ -0,0 +1,55 @@ +# Copyright 2013-2024 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# * Jan André Reuter +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.4' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.8.1'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb new file mode 100644 index 00000000000..de14ff81ce9 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.12.3'), + ('matplotlib', '3.9.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..246989eefdc --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.2.0-GCC-13.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.2.0' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('gperftools', '2.13'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9970f0a0afee1648890293321665e5b2efa04eaec9f1671fcf8048f456f5bb86'], +} + +local_external_absl = 'sed -i %(builddir)s/' + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + # using internal protobuf there is no matching pc file so requirement is removed: + 'preconfigopts': 'sed -i s/Requires.private.*// ../sentencepiece-%(version)s/sentencepiece.pc.in &&', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + # Unpredicable where pc files end up; including both lib and lib64 + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib64/pkgconfig:%(installdir)s/lib/pkgconfig/:' + '$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help | grep accept_language', # --help has exit code 1, so we check for output text + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb new file mode 100644 index 00000000000..820f9abf719 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.8.2' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9cf1e744b785fa673af5a7a1ce2f96d52dc03e14b6537097df86aa6266204556'] + +builddependencies = [ + ('Go', '1.22.1'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..36923c839cc --- /dev/null +++ b/easybuild/easyconfigs/s/SharedMeatAxe/SharedMeatAxe-1.0.1-GCC-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'SharedMeatAxe' +version = '1.0.1' + +homepage = 'https://github.com/simon-king-jena/SharedMeatAxe' +description = """This is an autotoolized shared library version of C MeatAxe 2.4.24, + a set of programs for computing with modular representations.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/simon-king-jena/SharedMeatAxe/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e1e802ef60f3280cdacb3de6d693ebd71b43af93e33c739de2697605c59b1a3b'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf --install && ' + +runtest = 'check' + +local_bins = [ + 'cfcomp', 'genmod', 'mkgraph', 'mkinc', 'orbrep', 'pwkond', 'symnew', 'zad', 'zcl', 'zcv', 'zfr', 'zmo', 'znu', + 'zpr', 'zro', 'zsp', 'zte', 'zuk', 'chop', 'mkcycl', 'mkhom', 'mksub', 'precond', 'rad', 'tcond', 'zbl', 'zcp', + 'zef', 'ziv', 'zmu', 'zor', 'zpt', 'zsc', 'zsy', 'ztr', 'zvp', 'decomp', 'mkdotl', 'mkhom_old', 'mktree', + 'pseudochop', 'soc', 'tuc', 'zcf', 'zct', 'zev', 'zkd', 'zmw', 'zpo', 'zqt', 'zsi', 'ztc', 'zts', +] + +sanity_check_paths = { + 'files': ['bin/%s' % bin for bin in local_bins] + ['include/meataxe.h', 'lib/libmtx.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ['mktree --help'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb new file mode 100644 index 00000000000..db9e6fe2fb3 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-CUDA-12.1.1-fast.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-CUDA-%(cudaver)s-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb new file mode 100644 index 00000000000..8e65da2a7d7 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2023a-fast.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('PyTorch', '2.1.2'), + ('matplotlib', '3.7.2'), +] + +preinstallopts = "sed -i 's/torch.*/torch/g' requirements.txt && " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..22eca6d4ed4 --- /dev/null +++ b/easybuild/easyconfigs/s/Single-cell-python-bundle/Single-cell-python-bundle-2024.02-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,247 @@ +easyblock = 'PythonBundle' + +name = 'Single-cell-python-bundle' +version = '2024.02' +versionsuffix = '-CUDA-12.1.1' + +homepage = (None) +description = """Bundle of tools for single-cell sequence analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), + ('CMake', '3.26.3'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyTorch', '2.1.2', versionsuffix), + ('scanpy', '1.9.8'), + ('scib', '1.1.4'), + ('scVelo', '0.3.1'), + ('CellTypist', '1.6.2'), + ('epiScanpy', '0.4.0'), + ('scCODA', '0.1.9'), + ('infercnvpy', '0.4.3'), + ('pySCENIC', '0.12.1-20240311'), + ('CellRank', '2.0.2', versionsuffix), + ('Squidpy', '1.4.1'), + ('Cassiopeia', '2.0.0'), + ('scvi-tools', '1.1.2', versionsuffix), + ('scArches', '0.6.1', versionsuffix), + ('scib-metrics', '0.5.1', versionsuffix), + # deps of exts: + ('umap-learn', '0.5.5'), # bbknn + ('scikit-learn', '1.3.1'), # bbknn, sc_toolbox + ('PyYAML', '6.0'), # sc_toolbox + ('typing-extensions', '4.9.0'), # sc_toolbox + ('adjustText', '0.7.3'), # sc_toolbox + ('python-parasail', '1.3.4'), # scirpy + ('graph-tool', '2.59'), # schist + ('Pyomo', '6.7.3'), # pertpy + ('mpmath', '1.3.0'), # blitzgsea +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('bbknn', '1.6.0', { + 'checksums': ['1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + ('anndata2ri', '1.3.1', { + 'checksums': ['0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42'], + }), + ('pypi-latest', '0.1.2', { + 'checksums': ['b195654567e6abaac6acfec37638d8e000838f419bc6b129962a896eedc4ed4e'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.4', { + 'modulename': 'slugify', + 'checksums': ['59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856'], + }), + ('prompt_toolkit', '3.0.36', { + 'checksums': ['3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('types-python-dateutil', '2.9.0.20240316', { + 'modulename': False, + 'checksums': ['5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202'], + }), + ('arrow', '1.3.0', { + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('cookiecutter', '2.6.0', { + 'checksums': ['db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('sc_toolbox', '0.12.3', { + 'checksums': ['6ca22a364c269a095114e620eb3c6da8aac1950d8f43f58ceea08005a09cc2cb'], + }), + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('altair', '5.2.0', { + 'checksums': ['2ad7f0c8010ebbc46319cc30febfb8e59ccf84969a201541c207bc3a4fa6cf81'], + }), + ('custom_inherit', '2.4.1', { + 'checksums': ['7052eb337bcce83551815264391cc4efc2bf70b295a3c52aba64f1ab57c3a8a2'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('pypng', '0.20220715.0', { + 'modulename': 'png', + 'checksums': ['739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1'], + }), + ('reportlab', '4.1.0', { + 'checksums': ['3a99faf412691159c068b3ff01c15307ce2fd2cf6b860199434874e002040a84'], + }), + ('toyplot', '1.0.3', { + 'checksums': ['7b7b2bc5784fd75e5c695300bffc80d568c83bebef543bb54e6e6c2229912edd'], + }), + ('toytree', '2.0.5', { + 'checksums': ['7be04ca310067e0e9737449700d6ab1b68b4379b64e2d22f2f7697a70030ceb0'], + }), + ('tascCODA', '0.1.3', { + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '/tensorflow-probability>=0.16/d' setup.py && ", + 'checksums': ['8c12ddccb72c41c96c6a5abceb52e7a76f439a9ab94fb092aa86ee3c1292383a'], + }), + ('harmonypy', '0.0.9', { + 'checksums': ['85bfdd4e6ec6e0fa8816a276639358d3598a40d60ba9f7a5d9dada8706be8c4d'], + }), + ('fbpca', '1.0', { + 'checksums': ['150677642479663f317fdbb5e06dab3f98721cf7031bb4a84113d7a631c472d1'], + }), + ('geosketch', '1.2', { + 'checksums': ['bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e'], + }), + ('python_circos', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'modulename': 'pycircos', + 'checksums': ['410eaffc4eb2933cd688897356813da23310f5e2f14a8bceb003e9b96faa715b'], + }), + ('mizani', '0.9.3', { + 'checksums': ['fb61339e9e4711850e902ca286b1ae75255f483823d891aa0515b426d56c606d'], + }), + ('plotnine', '0.12.4', { + 'checksums': ['adc41a672503594445a8fa19872799253bd0784cdbd5a1cc16657a1dd20ba905'], + }), + ('ktplotspy', '0.2.3', { + 'checksums': ['9a1e3646217e6e99f59ab2258dfd76120cf1f50880c9cb2f9005de397c00f0a9'], + }), + ('cellphonedb', '5.0.0', { + 'checksums': ['1c96173d8527f1655216d265fc50a28ea3360d70486afa5050e3f5565fa3a8cd'], + }), + ('decoupler', '1.6.0', { + 'checksums': ['dde501f4d3e55a260f716e51b871bee403bc8aaa6b66799df0e42dee0787b98d'], + }), + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('nodeenv', '1.9.0', { + 'checksums': ['07f144e90dae547bf0d4ee8da0ee42664a42a04e02ed68e06324348dafe4bdb1'], + }), + ('identify', '2.5.36', { + 'checksums': ['e5e00f54165f9047fbebeb4a560f9acfb8af4c88232be60a488e9b68d122745d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre_commit', '3.7.1', { + 'checksums': ['8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('liana', '1.2.0', { + 'checksums': ['be899c69bfcbf3d0f8b61c04c35f225ac6b11fe1ea80e6ed4bdc0e6212cb2379'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('scikit_build_core', '0.9.3', { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), + ('awkward-cpp', '33', { + 'checksums': ['550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8'], + }), + ('awkward', '2.6.4', { + 'checksums': ['ee0cb27c64150f368749983dda499c108848c64dc830912480eb37b78c04300f'], + }), + ('yamlordereddictloader', '0.4.2', { + 'checksums': ['36af2f6210fcff5da4fc4c12e1d815f973dceb41044e795e1f06115d634bca13'], + }), + ('airr', '1.5.0', { + 'checksums': ['febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42'], + }), + ('scirpy', '0.17.0', { + 'checksums': ['f61653a4f7387562ec89b00fbfd7cab762c0bf3320f21ccfc47df80a13cc5d41'], + }), + ('schist', '0.8.3', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/dawe/schist/archive/'], + 'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('jaxtyping', '0.2.29', { + 'checksums': ['e1cd916ed0196e40402b0638449e7d051571562b2cd68d8b94961a383faeb409'], + }), + ('equinox', '0.11.4', { + 'checksums': ['0033d9731083f402a855b12a0777a80aa8507651f7aa86d9f0f9503bcddfd320'], + }), + ('lineax', '0.0.4', { + 'checksums': ['e68f1eba2f352122fdce9adc0556684f31eb8364b1a00acee484dd6e44a34e5e'], + }), + ('jaxopt', '0.8.3', { + 'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'], + }), + ('ott_jax', '0.4.6', { + 'modulename': 'ott', + 'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'], + }), + ('sparsecca', '0.3.1', { + 'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'], + }), + ('PubChemPy', '1.0.4', { + 'checksums': ['24e9dc2fc90ab153b2764bf805e510b1410700884faf0510a9e7cf0d61d8ed0e'], + }), + ('blitzgsea', '1.3.42', { + 'checksums': ['dcc997b5d29d190d8632474f3bb57b5ead7fb1370b478c7f824b42782325a1ca'], + }), + ('pertpy', '0.7.0', { + 'checksums': ['273723b5b70f3cb714bb36d3234462014b72e133111eeaf08aa47153c9df14aa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..25fc18b7c63 --- /dev/null +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.16.0-foss-2023a.eb @@ -0,0 +1,107 @@ +easyblock = 'PythonBundle' + +name = 'SingleM' +version = '0.16.0' + +homepage = 'https://github.com/wwood/singlem' +description = """SingleM is a tool for profiling shotgun metagenomes. +It has a particular strength in detecting microbial lineages which are not in reference databases. +The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, +finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), + ('DIAMOND', '2.1.8'), + ('HMMER', '3.4'), + ('MAFFT', '7.520', '-with-extensions'), + ('OrfM', '0.7.1'), + ('mfqe', '0.5.0'), + ('KronaTools', '2.8.1'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('SRA-Toolkit', '3.0.10'), + ('Seqmagick', '0.8.6'), + ('ExpressBetaDiversity', '1.0.10'), + ('FastTree', '2.1.11'), + ('SQLAlchemy', '2.0.25'), + ('CD-HIT', '4.8.1'), + ('smafa', '0.8.0'), + ('prodigal', '2.6.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), + ('zenodo_backpack', '0.3.1', { + 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], + }), + ('bird_tool_utils', '0.4.1', { + 'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'], + }), + ('fastalite', '0.4.1', { + 'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + ('extern', '0.4.1', { + 'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'], + }), + ('graftm', '0.15.1', { + 'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'], + }), + ('singlem', version, { + 'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/graftM', 'bin/singlem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "graftM --help", + "singlem --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..608918e373c --- /dev/null +++ b/easybuild/easyconfigs/s/SpFFT/SpFFT-1.1.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'SpFFT' +version = '1.1.0' + +homepage = 'https://github.com/eth-cscs/SpFFT/' +description = """Sparse 3D FFT library with MPI, OpenMP, CUDA and ROCm support.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/SpFFT/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4673b3135aebfa1c440723226fe976d518ff881285b3d4787f1aa8210eac81e'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = "-DSPFFT_OMP=ON -DSPFFT_MPI=ON " + +sanity_check_paths = { + 'files': [ + 'include/spfft/spfft.h', + 'lib/libspfft.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c41639bc3ad --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '2.0.0' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('sphinxcontrib-jquery', '4.1', { + 'modulename': 'sphinxcontrib.jquery', + 'checksums': ['1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a'], + }), + ('sphinx_rtd_theme', version, { + 'checksums': ['bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb new file mode 100644 index 00000000000..0a822a69cbd --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-3.1.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '3.1.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['d096125ea3d987a55d17f7d4f8599ee2fd96bd2d0f033566e28ddfe248f730f9'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb index 88e067c36e8..576e48c80b4 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb index 10b926a9b61..5cc6a339682 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb index b2d223898c7..70a9918dc8e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb index 3dc0b200849..6d34fd7a476 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb index 6f536c566dd..e58b9c3ffef 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb index e0a01221b9d..ee9fd884627 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb index 8eb12670652..5fcc21050e5 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb index f614a665648..5cebe3f7c68 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb index 924f439ed4e..8edba3b1aa2 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb index 4b9a4923df9..a9926ab81d1 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb index 7f564c5a0fa..0d07710e238 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'http://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['http://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb index 69db79f2d43..e522a3ac747 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb index 242c281b919..822080c60fe 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Szip' version = '2.1.1' -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' +homepage = 'https://support.hdfgroup.org/doc_resource/SZIP/' description = """ Szip compression software, providing lossless compression of scientific data @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..cb33b614f6f --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.6.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('matplotlib', '3.7.2'), + ('anndata', '0.10.5.post1'), + ('h5py', '3.9.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('scikit-learn', '1.3.1'), + ('scvi-tools', '1.1.2', versionsuffix), + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('gdown', '5.1.0', { + 'checksums': ['550a72dc5ca2819fe4bcc15d80d05d7c98c0b90e57256254b77d0256b9df4683'], + }), + ('muon', '0.1.6', { + 'checksums': ['762feeb6f52f865cf79d0d0332cc742fe91c1885f668ce15794b62b3952b02f9'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + ('scHPL', '1.0.5', { + 'modulename': 'scHPL', + # unpin pandas and newick versions to be compatible with foss/2023a versions + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && sed -i 's/pandas>=1.1.2,<2/pandas/g' setup.py && ", + 'checksums': ['3eb62b2e65b1faba04b7bcb86f7bf6967a6301866a605551211b8f14fd27eced'], + }), + (name, version, { + 'checksums': ['187463c25781d5c5586c129ad137d96327a9f8604d530a696d5f568a9225d77c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb new file mode 100644 index 00000000000..5e7f3b40ba6 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.5-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scVelo' +version = '0.2.5' + +homepage = "https://scvelo.org" +description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), + ('PyTables', '3.8.0'), + ('statsmodels', '0.13.1'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('tqdm', '4.64.0'), + ('scanpy', '1.9.1'), # also provides anndata + ('Seaborn', '0.12.1'), + ('loompy', '3.0.7'), # also provides numpy-groupies + ('umap-learn', '0.5.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'scvelo', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['7e32d9e34245971330d69c12f4339cebe0acebb61e59a8b1aca9b369078b5207'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..b021ceb3c20 --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.5.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.5.1' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('jax', '0.4.25', versionsuffix), + ('scikit-learn', '1.3.1'), + ('scanpy', '1.9.8'), + ('python-igraph', '0.11.4'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.1', { + 'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('chex', '0.1.86', { + 'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..57e6f53d4c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.10.6-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.10.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('CMake', '3.29.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikit_build_core', version, { + 'checksums': ['5397db8f09ee050d145406c11deed06538bb0b261df95f8d2d6aaf8699f0126d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb index e355180eb49..dda0a838bf3 100644 --- a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = "Miscellaneous tools for data analysis and scientific computing" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pkgconf', '1.9.5'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb new file mode 100644 index 00000000000..5b6d65b6bb4 --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'scrublet' +version = '0.2.3' + +homepage = 'https://github.com/swolock/scrublet' +description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('tqdm', '4.66.1'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.3', { + 'checksums': ['9cbfebefe0a5f843eba29c6be4c84d601f4f41ad4ded0486f1b88c3b07739c15'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c434f381cfd --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '1.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('anndata', '0.10.5.post1'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('h5py', '3.9.0'), + ('jax', '0.4.25', versionsuffix), + ('Flax', '0.8.4', versionsuffix), + ('PyTorch-Lightning', '2.2.1', versionsuffix), + ('pyro-ppl', '1.9.0', versionsuffix), + ('ml-collections', '0.1.1'), +] + +use_pip = True + +exts_list = [ + ('mudata', '0.2.3', { + 'checksums': ['45288ac150bfc598d68acb7c2c1c43c38c5c39522107e04f7efbf3360c7f2035'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('numpyro', '0.15.0', { + 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('lightning', '2.1.4', { + 'checksums': ['0e45098c700fa28c604a11ae233ce181b44aeffce2404debebc2616118431d9f'], + }), + (name, version, { + 'modulename': 'scvi', + 'sources': ['scvi_tools-%(version)s.tar.gz'], + 'checksums': ['104a11a30e8996f5ceaa907b8c81b48b1f4b380d492ef2dd9b9a5577ed81b0f9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb index f79f5895f45..be427d2af9e 100644 --- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-1.1.2-foss-2023a.eb @@ -22,7 +22,7 @@ dependencies = [ ('PyTorch-Lightning', '2.2.1'), ('pyro-ppl', '1.9.0'), ('ml-collections', '0.1.1'), - ('Optax', '0.2.2'), + ('Flax', '0.8.4'), ] use_pip = True @@ -37,19 +37,6 @@ exts_list = [ ('numpyro', '0.15.0', { 'checksums': ['e16c9f47cc31e2aa259584a0b6c944312081d33ca92406022632ad584b0e600d'], }), - ('nest_asyncio', '1.6.0', { - 'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'], - }), - ('orbax_checkpoint', '0.5.15', { - 'modulename': 'orbax.checkpoint', - 'checksums': ['15195e8d1b381b56f23a62a25599a3644f5d08655fa64f60bb1b938b8ffe7ef3'], - }), - ('tensorstore', '0.1.60', { - 'checksums': ['88da8f1978982101b8dbb144fd29ee362e4e8c97fc595c4992d555f80ce62a79'], - }), - ('flax', '0.8.4', { - 'checksums': ['968683f850198e1aa5eb2d9d1e20bead880ef7423c14f042db9d60848cb1c90b'], - }), ('docrep', '0.3.2', { 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], }), diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index 8cbf2db9fe7..b2517ef684c 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.6.3', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb index 669229c8f11..044d56266ae 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing_extensions', '4.8.0', { diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb index a8ad0dc7ee9..b763364ba26 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.9.0-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('typing-extensions', '4.12.2', { diff --git a/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..3819e493fe2 --- /dev/null +++ b/easybuild/easyconfigs/s/sirocco/sirocco-2.1.0-GCC-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'sirocco' +version = '2.1.0' + +homepage = 'https://github.com/miguelmarco/SIROCCO2/' +description = """C++ library that allows to compute piecewise linear + approximations of the path followed by the root of a complex polynomial""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/miguelmarco/SIROCCO2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fd66ae94d73095f1355389c1d3d94222437bed87579d77667f50548bdd9fa9a'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('MPFR', '4.2.1'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/sirocco.h', + 'lib/libsirocco.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb new file mode 100644 index 00000000000..c34f17533e0 --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.17.2-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.17.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e5b235486b6901cd4ff0d94083f0e5eeacaef3a2893e1714769717ad488a3885'] + +dependencies = [ + ('Python', '3.10.4'), + ('SLEPc', version), + ('petsc4py', '3.17.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb new file mode 100644 index 00000000000..c161116802d --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.20.2-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.20.2' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['89ebd1964edd0eb63d4dbfa977d6f35408f4e19a3da290696fd1197901544bd8'] + +dependencies = [ + ('Python', '3.11.3'), + ('SLEPc', '3.20.1'), + ('petsc4py', '3.20.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb new file mode 100644 index 00000000000..f03005cda38 --- /dev/null +++ b/easybuild/easyconfigs/s/sleuth/sleuth-0.30.1-foss-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'sleuth' +version = '0.30.1' + +homepage = 'https://pachterlab.github.io/sleuth' +description = """Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pachterlab/sleuth/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c8efca5d726471cb71187e8db07097a50f63aadf42f6fa25c59e7eed635f982'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..342d27e7548 --- /dev/null +++ b/easybuild/easyconfigs/s/smafa/smafa-0.8.0-GCC-12.3.0.eb @@ -0,0 +1,235 @@ +easyblock = 'Cargo' + +name = 'smafa' +version = '0.8.0' + +homepage = 'https://github.com/wwood/smafa' +description = 'Biological sequence aligner for pre-aligned sequences.' + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wwood/smafa/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.8.0.tar.gz': '6f103ecd5cdf36fb61572a757732eeb07e905c61b497fa247c1a8397ee775c2d'}, + {'addr2line-0.22.0.tar.gz': '6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anstream-0.6.14.tar.gz': '418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b'}, + {'anstyle-1.0.7.tar.gz': '038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b'}, + {'anstyle-parse-0.2.4.tar.gz': 'c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4'}, + {'anstyle-query-1.1.0.tar.gz': 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'0.29.0'), + ('hash32', '0.2.1'), + ('heapless', '0.7.17'), + ('hermit-abi', '0.3.9'), + ('humantime', '2.1.0'), + ('is-terminal', '0.4.12'), + ('is_terminal_polyfill', '1.70.0'), + ('itoa', '1.0.11'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('miniz_oxide', '0.7.4'), + ('needletail', '0.5.1'), + ('object', '0.36.1'), + ('pkg-config', '0.3.30'), + ('postcard', '1.0.8'), + ('proc-macro2', '1.0.86'), + ('quote', '1.0.36'), + ('regex', '1.10.5'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('roff', '0.1.0'), + ('rustc-demangle', '0.1.24'), + ('rustc_version', '0.4.0'), + ('rustix', '0.38.34'), + ('ryu', '1.0.18'), + ('scopeguard', '1.2.0'), + ('semver', '1.0.23'), + ('serde', '1.0.204'), + ('serde_derive', '1.0.204'), + ('serde_json', '1.0.120'), + ('spin', '0.9.8'), + ('stable_deref_trait', '1.2.0'), + ('strsim', '0.11.1'), + ('syn', '1.0.109'), + ('syn', '2.0.71'), + ('synstructure', '0.12.6'), + ('tempfile', '3.10.1'), + ('termcolor', '1.4.1'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.2.4'), + ('utf8parse', '0.2.2'), + ('version-compare', '0.1.1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.8'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb new file mode 100644 index 00000000000..3b25c1e949f --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 00000000000..75446a8cbff --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.2.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'spektral' +version = '1.2.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s' % local_tf_version + +homepage = 'https://graphneural.network' +description = "Spektral is a Python library for graph deep learning, based on the Keras API and TensorFlow 2" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('TensorFlow', local_tf_version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['215f148e5d5067081bc28abe282bfd0942ed8be6d68f128fd7786006a884abf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb new file mode 100644 index 00000000000..9f26cade5d3 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.5.0-gfbf-2023b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.5.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('scikit-build-core', '0.9.3') +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject_metadata', '0.8.0', { + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('spglib', version, { + 'checksums': ['f8bb638897be91b9dbd4c085d9fde1f69048f5949e20f3832cb9438e57418d4b'], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a7e62a33f21 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# with thanks to akesandgren for the easyconfig for 2022a +# updated for 2022b by BEAR Software team at University of Birmingham +# update to v2.5.0 for GCC/12.3.0 by Pavel Tománek (Inuits) + +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.5.0' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6026f5e85106c0c9ee57e54b9399890d0f29982e20e96ede0428b3efbe6b914'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb new file mode 100644 index 00000000000..98308699678 --- /dev/null +++ b/easybuild/easyconfigs/s/spla/spla-1.6.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spla' +version = '1.6.1' + +homepage = 'https://github.com/eth-cscs/spla/' +description = """SPLA provides specialized functions for linear algebra computations with a C++ and C interface, +which are inspired by requirements in computational material science codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/eth-cscs/spla/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62b51e6ce05c41cfc1c6f6600410f9549a209c50f0331e1db41047f94493e02f'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +configopts = '-DBLA_VENDOR=FlexiBLAS' + +sanity_check_paths = { + 'files': [ + 'include/spla/spla.h', + 'lib/libspla.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb new file mode 100644 index 00000000000..0ce1edf2766 --- /dev/null +++ b/easybuild/easyconfigs/s/submitit/submitit-1.2.0-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'submitit' +version = '1.2.0' + +homepage = 'https://github.com/facebookincubator/submitit' +description = """ +Submitit is a lightweight tool for submitting Python functions +for computation within a Slurm cluster. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('typing_extensions', '4.12.2', { + 'checksums': ['1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8'], + }), + (name, version, { + 'checksums': ['16c099ed80943fbf942a7a37c6356a598b1f2b9d7ce40dd5fe058a6c7827e600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb new file mode 100644 index 00000000000..72d977763e9 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb @@ -0,0 +1,61 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('pybedtools', '0.9.0'), + ('Biopython', '1.81'), + ('Pillow', '9.4.0'), + ('ImageMagick', '7.1.0-53'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], + }), + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + (name, version, { + # unpin statistics dependency - it is old package and interfering with python lib statistics + 'preinstallopts': "sed -i 's/statistics//' setup.py && ", + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb new file mode 100644 index 00000000000..ab96be49230 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p5r0-foss-2023a.eb @@ -0,0 +1,90 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p5r0' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['2beb9793fb83d17de31b17f001f985fc30702c151e2ced614f5e0117e8e34aa0'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # provides numpy, scipy + ('matplotlib', '3.7.2'), + ('HDF5', '1.14.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S10.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + # Disable hyperthreading option + "-e 's/--use-hwthread-cpus//'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild.dyn", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) + +sanity_check_paths = { + 'files': ['builds/easybuild.dyn/bin/telemac2d', 'builds/easybuild.dyn/bin/telemac3d', + 'builds/easybuild.dyn/lib/libtelemac2d.%s' % SHLIB_EXT, + 'builds/easybuild.dyn/lib/libtelemac3d.%s' % SHLIB_EXT], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild.dyn/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild.dyn', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb new file mode 100644 index 00000000000..2c06e8c9c8f --- /dev/null +++ b/easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'TF-COMB' +version = '1.1' + +homepage = 'https://github.com/loosolab/TF-COMB' +description = """Transcription Factor Co-Occurrence using Market Basket analysis.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('tqdm', '4.64.1'), + ('Pysam', '0.21.0'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), + ('Graphviz', '8.1.0'), + ('statsmodels', '0.14.0'), + ('dill', '0.3.7'), + ('Seaborn', '0.12.2'), + ('IPython', '8.14.0'), + ('TOBIAS', '0.16.1'), + ('python-louvain', '0.16'), + ('GOATOOLS', '1.4.5'), + ('qnorm', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +# remove graphviz from deps - the pip check failing, should be "import gv" +local_tfcomb_preinstallopts = "sed -i '70d' setup.py && " +# fix "import graphviz" to "import gv" +local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && " + +exts_list = [ + ('uropa', '4.0.3', { + 'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'], + }), + (name, version, { + 'preinstallopts': local_tfcomb_preinstallopts, + 'modulename': 'tfcomb', + 'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb new file mode 100644 index 00000000000..ac13f1e800f --- /dev/null +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.11.3-foss-2023a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'TINKER' +version = '8.11.3' + +homepage = 'https://dasher.wustl.edu/tinker' +description = """The Tinker molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +srcdir = 'cmake' + +test_cmd = 'cd ../tinker/test/ && ' +# fix path to executables in .run test scripts +test_cmd += r"sed -i 's|\.\./bin|../../easybuild_obj|g' *.run && " +# run all .run scripts +# manually compare test results with .log files in test dir +# (ifabp succeeds but exits with a memory error) +test_cmd += 'for x in *.run; do echo "START TEST: $x" && ./$x; done' + +postinstallcmds = ['cd %(start_dir)s && cp -a params perl python %(installdir)s'] + +sanity_check_paths = { + 'files': ['lib/libtinker.a'], + 'dirs': ['bin', 'params', 'perl', 'python'], +} + +# (no sanity_check_commands since all programs require multiple other inputs) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb new file mode 100644 index 00000000000..9150965319e --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.16.1' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Seaborn', '0.12.2'), + ('Pysam', '0.21.0'), + ('pybedtools', '0.9.0'), + ('boto3', '1.26.163'), + ('pyBigWig', '0.3.22'), + ('scikit-learn', '1.2.1'), + ('PyYAML', '6.0'), + ('XlsxWriter', '3.1.2'), + ('svist4get', '1.3.1'), + ('adjustText', '0.7.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('tobias', version, { + # remove pyBigWig dependency - pip_check fails with "import pybigwig" + 'preinstallopts': "sed -i '81d' setup.py && ", + 'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'], + }), +] + +sanity_check_commands = ["python -c 'import pyBigWig'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cbf3e47917e --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..7b2f4888b23 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,178 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.15.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('Bazel', '6.1.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # Protobuf disabled since 2.13.0 easyconfigs: + # Compiling with system protobuf don't seem to work, see: + # https://github.com/tensorflow/tensorflow/issues/61593 + # ('protobuf', '24.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('ml_dtypes', '0.3.2'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + ('tensorboard', '2.15.1'), +] + +# Dependencies created and updated using findPythonDeps, see: +# https://docs.easybuild.io/api/easybuild/scripts/findPythonDeps +# Notable changes since 2.13.0-foss-2023a +# - tensoboard-wit deprecated as of tensorboard 2.13.0 (tensorboard@33abcb54d7) +# - portpicker for tests no longer needed (TF@e85860e838) +# - opt_einsum now comes from ml_dtypes +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('tensorflow-estimator', '2.15.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], + }), + ('keras', '2.15.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.15.1_remove-libclang-dep.patch', + 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', + 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', + 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_fix-cuda_build_defs.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', + 'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch' + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': ( + '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_tag_filters_gpu': ( + 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only' + ), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ', + 'testopts_gpu': ( + '--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small ' + '--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute ' + ), + 'with_xla': True, + 'checksums': [ + {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch': + 'd8810d5b875de5be8603afd743774ce9dd8c0d4a82314c7fe2f284a080be7498'}, + {'TensorFlow-2.15.1_remove-libclang-dep.patch': + '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, + {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': + 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, + {'TensorFlow-2.15.1_add-default-shell-env.patch': + '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, + {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': + '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, + {'TensorFlow-2.15.1_fix-pybind11-build.patch': + '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_fix-cuda_build_defs.patch': + '091581a7c4fc2fc7af282cab6661632c29029d2f36eccb6695ffa5783e065f88'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, + {'TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch': + 'f78aa0e8f814a57e8d2e6b24ff095df49e8654aadb797393fa95a9378d0aa662'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb index 014f3bbd7a5..ebca59072d6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1-foss-2023a.eb @@ -47,7 +47,7 @@ dependencies = [ ('libpng', '1.6.39'), ('snappy', '1.1.10'), ('zlib', '1.2.13'), - ('grpcio', '1.57.0'), + ('tensorboard', '2.15.1'), ] # Dependencies created and updated using findPythonDeps, see: @@ -57,7 +57,6 @@ dependencies = [ # - portpicker for tests no longer needed (TF@e85860e838) # - opt_einsum now comes from ml_dtypes exts_list = [ - ('wrapt', '1.14.1', { 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], }), @@ -68,48 +67,6 @@ exts_list = [ 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['aedf21eec7fb2dc91150fc91a1ce12bc44dbb72278a08b58e79ff87c9e28f153'], }), - ('Werkzeug', '3.0.2', { - 'source_tmpl': SOURCELOWER_TAR_GZ, - 'checksums': ['e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d'], - }), - ('tensorboard-data-server', '0.7.2', { - 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', - 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], - }), - ('Markdown', '3.6', { - 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('requests-oauthlib', '2.0.0', { - 'checksums': ['b3dffaebd884d8cd778494369603a9e7b58d29111bf6b41bdc2dcd87203af4e9'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.4.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['831dbcea1b177b28c9baddf4c6d1013c24c3accd14a1873fffaa6a2e905f17b6'], - }), - ('cachetools', '5.3.3', { - 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], - }), - ('google-auth', '2.29.0', { - 'modulename': 'google.auth', - 'checksums': ['672dff332d073227550ffc7457868ac4218d6c500b155fe6cc17d2b13602c360'], - }), - ('google-auth-oauthlib', '1.2.0', { - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('absl-py', '2.1.0', { - 'modulename': 'absl', - 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], - }), - ('tensorboard', '2.15.2', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'checksums': ['a6f6443728064d962caea6d34653e220e34ef8df764cb06a8212c17e1a8f0622'], - }), ('keras', '2.15.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['2dcc6d2e30cf9c951064b63c1f4c404b966c59caf09e01f3549138ec8ee0dd1f'], @@ -128,23 +85,17 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - # Optional profile plugin + dependency - ('gviz-api', '1.10.0', { - 'source_tmpl': 'gviz_api-%(version)s.tar.gz', - 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], - }), - ('tensorboard-plugin-profile', '2.15.1', { - 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', - 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], - }), (name, version, { 'patches': [ 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.15.1_remove-libclang-dep.patch', 'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.15.1_add-default-shell-env.patch', + 'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch', 'TensorFlow-2.15.1_fix-flatbuffer-license.patch', 'TensorFlow-2.15.1_fix-pybind11-build.patch', + 'TensorFlow-2.15.1_disable-avx512-extensions.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -185,27 +136,24 @@ exts_list = [ {'v2.15.1.tar.gz': 'f36416d831f06fe866e149c7cd752da410a11178b01ff5620e9f265511ed57cf'}, {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, {'TensorFlow-2.15.1_remove-libclang-dep.patch': '871b2f0221b7a150ac9f563ffad7187e052a7eedd95c20fb4524987d7edb6f21'}, {'TensorFlow-2.15.1_remove-io-gcs-filesystem-dep.patch': 'eba7351a4b0696c589b9c507bacb0257ebce8c39fde39ab72d5d6a69deaaec02'}, {'TensorFlow-2.15.1_add-default-shell-env.patch': '3d5196b4bf2e91048dc8a18f9e8f487a223fcd973d6302e80b0d4000ea3d652b'}, + {'TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch': + '761059e5f5f5eeeef8aed5517a7685a0eb0a9193d4afe8d45237527681c9c0a3'}, {'TensorFlow-2.15.1_fix-flatbuffer-license.patch': '2c04d5095977a628a238dbf93c5fada7159c86752a7183e64e0cf7c7ab00caf4'}, {'TensorFlow-2.15.1_fix-pybind11-build.patch': '3bb350ac92ab99c63c951c96b3b0160699f5f16822b64f72111ebfd2275cafce'}, + {'TensorFlow-2.15.1_disable-avx512-extensions.patch': + '506ceecff67237eed9cd9e9e114bc1461f35a343f77f83cb3dab710aa701dc0f'}, ], }), ] -# Taken from tensorboard-2.15.1-gfbf-2023a.eb: -# Relax restriction on protobuf dependency as issue was fixed -# in https://github.com/protocolbuffers/upb/pull/1514 -# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 -postinstallcmds = [ - 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + - '%(installdir)s/lib/python%(pyshortver)s/site-packages/tensorboard-2.15.2.dist-info/METADATA', -] - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch new file mode 100644 index 00000000000..7778d2b4a91 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +index 5301914ad37..8923bfed7bf 100644 +--- a/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h ++++ b/third_party/xla/third_party/tsl/tsl/framework/fixedpoint/FixedPoint.h +@@ -20,7 +20,7 @@ limitations under the License. + #include "tsl/framework/fixedpoint_types.h" + + // Use optimized implementations whenever available +-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "tsl/framework/fixedpoint/PacketMathAVX512.h" + #include "tsl/framework/fixedpoint/TypeCastingAVX512.h" + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch new file mode 100644 index 00000000000..9cc742e53d0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_disable-tf32-in-fused-matmul-tests.patch @@ -0,0 +1,46 @@ +Fixes failing FusedMatMul test on certain GPU models + +diff --git a/tensorflow/core/kernels/matmul_op_test.cc b/tensorflow/core/kernels/matmul_op_test.cc +index 8d81d4c796e..2de0365f067 100644 +--- a/tensorflow/core/kernels/matmul_op_test.cc ++++ b/tensorflow/core/kernels/matmul_op_test.cc +@@ -21,6 +21,7 @@ limitations under the License. + #include "tensorflow/core/framework/tensor.h" + #include "tensorflow/core/kernels/ops_testutil.h" + #include "tensorflow/core/lib/core/status_test_util.h" ++#include "tensorflow/core/platform/tensor_float_32_utils.h" + #include "tensorflow/core/platform/test.h" + #include "tensorflow/core/platform/test_benchmark.h" + #include "tensorflow/core/protobuf/rewriter_config.pb.h" +@@ -287,6 +288,7 @@ TYPED_TEST_SUITE_P(FusedMatMulWithBiasOpTest); + // -------------------------------------------------------------------------- // + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 128, 64, false, false); + this->VerifyMatMulWithBias(256, 128, 64, true, false); + this->VerifyMatMulWithBias(256, 128, 64, false, true); +@@ -294,6 +296,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(1, 256, 256, false, false); + this->VerifyMatMulWithBias(4, 128, 256, false, false); + this->VerifyMatMulWithBias(1, 256, 256, true, false); +@@ -302,6 +305,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x256) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x256x1) { ++ tensorflow::enable_tensor_float_32_execution(false); + this->VerifyMatMulWithBias(256, 256, 1, false, false); + this->VerifyMatMulWithBias(256, 128, 4, false, false); + this->VerifyMatMulWithBias(256, 256, 1, true, false); +@@ -314,6 +318,7 @@ TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul1x256x1) { + } + + TYPED_TEST_P(FusedMatMulWithBiasOpTest, MatMul256x128x64WithActivation) { ++ tensorflow::enable_tensor_float_32_execution(false); + for (const string& activation : {"Relu", "Relu6", "Elu", "LeakyRelu"}) { + this->VerifyConv2DWithBiasAndActivation(256, 128, 64, false, false, + activation); diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch new file mode 100644 index 00000000000..514f215cde9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-AVX512-eigen-compilation.patch @@ -0,0 +1,47 @@ +Fix a compilation error for CPUs with AVX512 features where an issue in Eigen leads to +> invalid 'static_cast' from type 'const Eigen::internal::eigen_packet_wrapper<__vector(4) long long int, 1>' to type '__vector(16) float' + +See https://gitlab.com/libeigen/eigen/-/issues/2829 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-avx512.patch b/third_party/eigen3/fix-avx512.patch +new file mode 100644 +index 00000000000..0650d52a0c9 +--- /dev/null ++++ b/third_party/eigen3/fix-avx512.patch +@@ -0,0 +1,22 @@ ++diff --git a/Eigen/src/Core/arch/AVX512/TypeCasting.h b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++index 02c56282f..e253e6b49 100644 ++--- a/Eigen/src/Core/arch/AVX512/TypeCasting.h +++++ b/Eigen/src/Core/arch/AVX512/TypeCasting.h ++@@ -145,8 +145,6 @@ template<> EIGEN_STRONG_INLINE Packet8bf preinterpret(con ++ return _mm256_castsi256_si128(a); ++ } ++ ++-#ifndef EIGEN_VECTORIZE_AVX512FP16 ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16h& a) { ++ return half2float(a); ++ } ++@@ -155,8 +153,6 @@ template<> EIGEN_STRONG_INLINE Packet16h pcast(const Packe ++ return float2half(a); ++ } ++ ++-#endif ++- ++ template<> EIGEN_STRONG_INLINE Packet16f pcast(const Packet16bf& a) { ++ return Bf16ToF32(a); ++ } +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index d1d8d4ac486..da549e37432 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,6 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", ++ patch_file = ["//third_party/eigen3:fix-avx512.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch new file mode 100644 index 00000000000..0982df21bb9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_fix-cuda_build_defs.patch @@ -0,0 +1,40 @@ +Backport cuda_build_defs path fix for TF 2.15, see: + +https://github.com/tensorflow/tensorflow/commit/1536f2ca228099f0cf7793d3031d9b9bebbf03ed + +diff --git a/third_party/nccl/system.BUILD.tpl b/third_party/nccl/system.BUILD.tpl +index 405d1e7298b..6e2a22a950b 100644 +--- a/third_party/nccl/system.BUILD.tpl ++++ b/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@org_tensorflow//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/nccl/system.BUILD.tpl +index 13328fdeeac..6e2a22a950b 100644 +--- a/third_party/xla/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_xla//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + +diff --git a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +index b45138eaa79..6e2a22a950b 100644 +--- a/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl ++++ b/third_party/xla/third_party/tsl/third_party/nccl/system.BUILD.tpl +@@ -1,6 +1,6 @@ + load("@bazel_skylib//rules:write_file.bzl", "write_file") + load( +- "@local_tsl//tensorflow/platform/default:cuda_build_defs.bzl", ++ "@local_tsl//tsl/platform/default:cuda_build_defs.bzl", + "cuda_rpath_flags" + ) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..7c6d72c89c9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.15.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index a1531f55cca..3b9c977dcc4 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1626,22 +1626,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 2cfb8444ca4..daa5022fb1f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -40,9 +40,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 54fdbc44964..7a4a7766ca6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -42,9 +42,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -exts_default_options = { - 'sanity_pip_check': True, -} +sanity_pip_check = True use_pip = True # Dependencies created and updated using findPythonDeps.sh: diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..4069dc5a048 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.14-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.14' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['8ffdb720f47a6ca6107eac2dd877e30b0ef7fac14f3a84ebbd0b3612cee41a94'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Tcl', version), + ('X11', '20240607'), + ('zlib', '1.3.1'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..00f02ee6424 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.12.3-GCCcore-13.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.12.3' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'] + +builddependencies = [ + ('binutils', '2.42'), + ('libffi', '3.4.5'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Tk', '8.6.14'), + ('zlib', '1.3.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..a70ecf2a901 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'RubyGem' + +name = 'Transrate' +version = '1.0.3' + +homepage = 'https://hibberdlab.com/transrate' +description = """Transrate is software for de-novo transcriptome assembly quality analysis. + It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, + reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, + filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/blahah/transrate/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Transrate-1.0.3_undefined_method_fix.patch'] +checksums = [ + {'v1.0.3.tar.gz': '2ccb101cfab5a33586ea9e62af2b2f14caf6bc016724d1fef796b427e39fe100'}, + {'Transrate-1.0.3_undefined_method_fix.patch': 'ead5e51318d6d810fb11b783d517ea38648f62ae2bdd5f3f4dac7baa9ae94d95'}, +] + +dependencies = [ + ('Ruby', '3.3.0'), + ('crb-blast', '0.6.9'), + ('colorize', '0.7.7'), + ('yell', '2.2.2'), +] + +# requirement is too strict +preinstallopts = """sed -i "s/'yell', '~> 2.0',/'yell',/g" transrate.gemspec && """ + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch new file mode 100644 index 00000000000..47526bd2242 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3_undefined_method_fix.patch @@ -0,0 +1,42 @@ +to avoid the `terminal_columns': undefined method `winsize' for nil (NoMethodError)` error +Author: Petr Král (INUITS) +--- lib/transrate/cmdline.rb.orig 2016-06-06 15:10:26.000000000 +0200 ++++ lib/transrate/cmdline.rb 2024-07-25 11:23:20.250369056 +0200 +@@ -87,11 +87,6 @@ + end + end + +- def terminal_columns +- require 'io/console' +- IO.console.winsize.last +- end +- + def help_message + <<-EOS + +@@ -117,19 +112,17 @@ + end + + def transrate_banner +- if terminal_columns > 70 +- txp = '░▓▓▓^▓▓▓░' +- toptxp = txp.green +- midtxp = txp.yellow +- bottxp = txp.red +- puts <<-EOS ++ txp = '░▓▓▓^▓▓▓░' ++ toptxp = txp.green ++ midtxp = txp.yellow ++ bottxp = txp.red ++ puts <<-EOS + _ _ + | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___ + #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp} + #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp} + #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp} +- EOS +- end ++ EOS + "" + end + diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch new file mode 100644 index 00000000000..13d736b4bfc --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-disable_rocm_support.patch @@ -0,0 +1,88 @@ +Disable experimental support for AMD GPUs +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/CMakeLists.txt triton-2.1.0/CMakeLists.txt +--- triton-2.1.0.orig/CMakeLists.txt 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/CMakeLists.txt 2024-09-01 10:40:17.863374000 +0200 +@@ -70,7 +70,7 @@ + AMDGPUInfo AMDGPUcodegen + ) + else() +- find_package(LLVM 11 REQUIRED COMPONENTS "nvptx;amdgpu") ++ find_package(LLVM 11 REQUIRED COMPONENTS "nvptx") + endif() + + message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}") +@@ -89,9 +89,7 @@ + LLVMNVPTXCodeGen + LLVMNVPTXDesc + LLVMNVPTXInfo +- LLVMAMDGPUDisassembler + LLVMMCDisassembler +- LLVMAMDGPUCodeGen + LLVMMIRParser + LLVMGlobalISel + LLVMSelectionDAG +@@ -116,10 +114,7 @@ + LLVMObject + LLVMTextAPI + LLVMBitReader +- LLVMAMDGPUAsmParser + LLVMMCParser +- LLVMAMDGPUDesc +- LLVMAMDGPUUtils + LLVMMC + LLVMDebugInfoCodeView + LLVMDebugInfoMSF +@@ -127,7 +122,6 @@ + LLVMRemarks + LLVMBitstreamReader + LLVMBinaryFormat +- LLVMAMDGPUInfo + LLVMSupport + LLVMDemangle + LLVMPasses +diff -ur triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp +--- triton-2.1.0.orig/lib/Target/HSACO/HSACOTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/HSACO/HSACOTranslation.cpp 2024-09-02 21:27:09.233712000 +0200 +@@ -37,13 +37,6 @@ + + namespace { + +-void init_llvm() { +- LLVMInitializeAMDGPUTarget(); +- LLVMInitializeAMDGPUTargetInfo(); +- LLVMInitializeAMDGPUTargetMC(); +- LLVMInitializeAMDGPUAsmParser(); +- LLVMInitializeAMDGPUAsmPrinter(); +-} + + std::unique_ptr + initialize_module(llvm::Module *module, const std::string &triple, +@@ -155,7 +148,6 @@ + llir_to_amdgcn_and_hsaco(llvm::Module *module, std::string gfx_arch, + std::string gfx_triple, std::string gfx_features) { + +- init_llvm(); + + // verify and store llvm + auto module_obj = llvm::CloneModule(*module); +diff -ur triton-2.1.0.orig/python/src/triton.cc triton-2.1.0/python/src/triton.cc +--- triton-2.1.0.orig/python/src/triton.cc 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/src/triton.cc 2024-09-01 10:41:29.146862440 +0200 +@@ -60,7 +60,6 @@ + enum backend_t { + HOST, + CUDA, +- ROCM, + }; + + void init_triton_runtime(py::module &&m) { +@@ -68,7 +67,6 @@ + py::enum_(m, "backend", py::module_local()) + .value("HOST", HOST) + .value("CUDA", CUDA) +- .value("ROCM", ROCM) + .export_values(); + } + diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..a1cdbe87df3 --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonPackage' + +name = 'Triton' +version = '2.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://triton-lang.org/' + +description = """Triton is a language and compiler for parallel programming. It aims to provide a +Python-based programming environment for productively writing custom DNN compute +kernels capable of running at maximal throughput on modern GPU hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'openai' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-disable_rocm_support.patch', + '%(name)s-%(version)s-use_eb_env_python_build.patch', +] +checksums = [ + {'v2.1.0.tar.gz': '4338ca0e80a059aec2671f02bfc9320119b051f378449cf5f56a1273597a3d99'}, + {'Triton-2.1.0-disable_rocm_support.patch': 'e4d7c0947c3287b3f0871a004e8b483963f637c9fa3ef6212ac3a34660de2a7c'}, + {'Triton-2.1.0-use_eb_env_python_build.patch': 'd68bf766c699ad6a778d9449d3bccdadc2f20f1f86ba13e1359ad297b12fbf7c'}, +] + +builddependencies = [ + ('Clang', '17.0.0_20230515', versionsuffix), # this is the exact commit that would be downloaded by Triton + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +start_dir = 'python' + +preinstallopts = 'export LLVM_INCLUDE_DIRS=$EBROOTCLANG/include && ' +preinstallopts += 'export LLVM_LIBRARY_DIR=$EBROOTCLANG/lib && ' +preinstallopts += 'export LLVM_SYSPATH=$EBROOTCLANG && ' +preinstallopts += 'export TRITON_BUILD_WITH_CLANG_LLD=1 && ' + +# make pip print output of cmake +installopts = "-v " + +sanity_pip_check = True + +modluafooter = 'setenv("TRITON_PTXAS_PATH", pathJoin(os.getenv("CUDA_HOME"), "bin", "ptxas"))' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch new file mode 100644 index 00000000000..650134e73be --- /dev/null +++ b/easybuild/easyconfigs/t/Triton/Triton-2.1.0-use_eb_env_python_build.patch @@ -0,0 +1,93 @@ +Fix Triton cmake build to use dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp +--- triton-2.1.0.orig/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/lib/Target/LLVMIR/LLVMIRTranslation.cpp 2024-09-02 19:46:06.574421829 +0200 +@@ -35,6 +35,7 @@ + #endif + #include + #include ++#include // for getenv + + namespace fs = std::filesystem; + +@@ -177,6 +178,7 @@ + } + + if (!funcs.empty()) { ++ std::filesystem::path cuda_home = std::getenv("CUDA_HOME"); + static const std::string libdevice = "libdevice"; + // first search for environmental path + std::string env_path = ::triton::tools::getenv("TRITON_LIBDEVICE_PATH"); +@@ -189,8 +191,7 @@ + // `triton/third_party/cuda/lib/libdevice.10.bc` + static const auto this_library_path = getThisLibraryPath(); + static const auto runtime_path = +- this_library_path.parent_path().parent_path() / "third_party" / "cuda" / +- "lib" / "libdevice.10.bc"; ++ cuda_home / "nvvm" / "libdevice" / "libdevice.10.bc"; + if (fs::exists(runtime_path)) { + externLibs.try_emplace(libdevice, runtime_path.string()); + } else { +diff -ur triton-2.1.0.orig/python/setup.py triton-2.1.0/python/setup.py +--- triton-2.1.0.orig/python/setup.py 2023-09-01 08:28:27.000000000 +0200 ++++ triton-2.1.0/python/setup.py 2024-09-02 18:16:58.044760300 +0200 +@@ -202,13 +202,13 @@ + + def build_extension(self, ext): + lit_dir = shutil.which('lit') +- user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ +- os.getenv("HOMEPATH") or None +- if not user_home: +- raise RuntimeError("Could not find user home directory") +- triton_cache_path = os.path.join(user_home, ".triton") ++ # user_home = os.getenv("HOME") or os.getenv("USERPROFILE") or \ ++ # os.getenv("HOMEPATH") or None ++ # if not user_home: ++ # raise RuntimeError("Could not find user home directory") ++ # triton_cache_path = os.path.join(user_home, ".triton") + # lit is used by the test suite +- thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) ++ # thirdparty_cmake_args = get_thirdparty_packages(triton_cache_path) + extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.path))) + # create build directories + if not os.path.exists(self.build_temp): +@@ -216,8 +216,9 @@ + # python directories + python_include_dir = sysconfig.get_path("platinclude") + cmake_args = [ ++ "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON", + "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON", +- "-DLLVM_ENABLE_WERROR=ON", ++ # "-DLLVM_ENABLE_WERROR=ON", + "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir, + "-DTRITON_BUILD_TUTORIALS=OFF", + "-DTRITON_BUILD_PYTHON_MODULE=ON", +@@ -227,7 +228,7 @@ + ] + if lit_dir is not None: + cmake_args.append("-DLLVM_EXTERNAL_LIT=" + lit_dir) +- cmake_args.extend(thirdparty_cmake_args) ++ # cmake_args.extend(thirdparty_cmake_args) + + # configuration + cfg = get_build_type() +@@ -245,7 +246,7 @@ + build_args += ["--", "/m"] + else: + cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg] +- max_jobs = os.getenv("MAX_JOBS", str(2 * os.cpu_count())) ++ max_jobs = os.getenv("MAX_JOBS", str(len(os.sched_getaffinity(0)))) + build_args += ['-j' + max_jobs] + + if check_env_flag("TRITON_BUILD_WITH_CLANG_LLD"): +@@ -262,7 +263,7 @@ + subprocess.check_call(["cmake", "--build", "."] + build_args, cwd=cmake_dir) + + +-download_and_copy_ptxas() ++# download_and_copy_ptxas() + + + setup( diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5b532a99e9f --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.1.2' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + '98629cd2b676df5d30df51c69edd97cf99b395c3080cc55e2f997ac33a7d40de', # 3.0.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), +] + +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('libglvnd', '1.7.0'), + ('OpenSSL', '3', '', SYSTEM), +] + +osdependencies = [('pam-devel', 'libpam0g-dev')] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ['rm -rf %(installdir)s/etc/turbovncserver-security.conf'] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..63408d65ee7 --- /dev/null +++ b/easybuild/easyconfigs/t/tdlib/tdlib-0.9.3-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'tdlib' +version = '0.9.3' + +homepage = 'https://github.com/freetdi/tdlib/' +description = """treedec provides tree decomposition algorithms.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/freetdi/tdlib/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1730c98f41dcb23bbd0bd8de9dbec51df015304f28a38935848925901594ae8'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Boost', '1.83.0'), + ('Python', '3.11.5'), +] + +preconfigopts = 'autoreconf --install && ' + +sanity_check_paths = { + 'files': [ + 'include/treedec/combinations.hpp', + ], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb new file mode 100644 index 00000000000..304e56b390f --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2022b.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +postinstallpatches = [ + ('tensorboard-2.10_jupyterhub-support.patch', 'lib/python%(pyshortver)s/site-packages'), +] +checksums = [ + {'tensorboard-2.10_jupyterhub-support.patch': + '50a292e6ee518aecb5644595e0f3db4867be4f82e328e008e5a3f6a1f19baf87'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), + ('grpcio', '1.57.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.15.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['84bb33e446eb4a9c0616f669fc6a42cdd40eadd9ae1d74bf756f4f0479993273'], + }), + ('Werkzeug', '3.0.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +# see also: https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb index c86b16b035f..efede874267 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True +# avoid pip check fail when tensorflow-probability is a dependency +local_postinstallcmds = "cd %(installdir)s/lib/python%(pyshortver)s/site-packages && " +local_postinstallcmds += "mv tfp_nightly-%(version)s.dist-info tensorflow_probability-%(version)s.dist-info && " +local_postinstallcmds += "sed -i 's/Name: tfp-nightly/Name: %(name)s/' " +local_postinstallcmds += "tensorflow_probability-%(version)s.dist-info/METADATA" + exts_list = [ ('cloudpickle', '3.0.0', { 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], @@ -37,6 +43,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], + 'postinstallcmds': [local_postinstallcmds], }), ] diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..94cf0915ff9 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.4' +_tessdata_ver = '4.1.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '%s.tar.gz' % _tessdata_ver, + 'filename': 'tessdata_best-%s.tar.gz' % _tessdata_ver, + }, +] +checksums = [ + {'5.3.4.tar.gz': '141afc12b34a14bb691a939b4b122db0d51bd38feda7f41696822bacea7710c7'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5') +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('Leptonica', '1.84.1'), + ('libarchive', '3.6.2'), + ('ICU', '73.2'), + ('fontconfig', '2.14.2'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('Pango', '1.50.14'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-*/configs', + 'rm -rf %(builddir)s/tessdata_best-*/tessconfigs', + 'mv %(builddir)s/tessdata_best-*/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'share/tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..aadc225d0fa --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0', versionsuffix), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b9d92f49462 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.5-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.5' + +homepage = 'https://github.com/tqdm/tqdm' +description = "A fast, extensible progress bar for Python and CLI" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..552279e3ffe --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.11.0-GCCcore-13.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.11.0' + +homepage = 'https://github.com/python/typing_extensions' +description = "Typing Extensions - Backported and Experimental Type Hints for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0'] + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..34271e18021 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.16.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.16.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.16.0.tar.gz': 'f73770d3b583c91aba5fb07557e655ead0786e057018bfe42f0ebe8716e9d28c'}, + {'UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch': + 'aa5bab38c188276958dd6829da4929ed9ff0b67cd55665b4459521cf3fbbe46d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('UCX', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('GDRCopy', '2.4.1'), +] + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch new file mode 100644 index 00000000000..92973cd7f80 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.16.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,93 @@ +diff --git a/configure.ac b/configure.ac +index 8d8da54..2765fe0 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -30,13 +30,13 @@ valgrind_libpath="" + AC_USE_SYSTEM_EXTENSIONS + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff --git a/src/ucm/cuda/Makefile.am b/src/ucm/cuda/Makefile.am +index 00bd224..22e719f 100644 +--- a/src/ucm/cuda/Makefile.am ++++ b/src/ucm/cuda/Makefile.am +@@ -9,7 +9,7 @@ if HAVE_CUDA + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la $(CUDA_LIBS) $(CUDART_LIBS) ++libucm_cuda_la_LIBADD = -lucm $(CUDA_LIBS) $(CUDART_LIBS) + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff --git a/src/ucm/rocm/Makefile.am b/src/ucm/rocm/Makefile.am +index f9e183f..dcd1587 100644 +--- a/src/ucm/rocm/Makefile.am ++++ b/src/ucm/rocm/Makefile.am +@@ -10,7 +10,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff --git a/src/uct/cuda/Makefile.am b/src/uct/cuda/Makefile.am +index 00899ab..dcee6b0 100644 +--- a/src/uct/cuda/Makefile.am ++++ b/src/uct/cuda/Makefile.am +@@ -11,8 +11,8 @@ module_LTLIBRARIES = libuct_cuda.la + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la \ ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct \ + $(CUDA_LIBS) $(CUDART_LIBS) $(NVML_LIBS) + + noinst_HEADERS = \ +diff --git a/src/uct/cuda/gdr_copy/Makefile.am b/src/uct/cuda/gdr_copy/Makefile.am +index 47602c7..601cb9f 100644 +--- a/src/uct/cuda/gdr_copy/Makefile.am ++++ b/src/uct/cuda/gdr_copy/Makefile.am +@@ -9,7 +9,7 @@ module_LTLIBRARIES = libuct_cuda_gdrcopy.la + libuct_cuda_gdrcopy_la_CPPFLAGS = $(BASE_CPPFLAGS) $(GDR_COPY_CPPFLAGS) + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) + libuct_cuda_gdrcopy_la_LDFLAGS = $(GDR_COPY_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la \ + $(GDR_COPY_LIBS) + +diff --git a/src/uct/rocm/Makefile.am b/src/uct/rocm/Makefile.am +index c7abce1..257e33f 100644 +--- a/src/uct/rocm/Makefile.am ++++ b/src/uct/rocm/Makefile.am +@@ -8,8 +8,7 @@ if HAVE_ROCM + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ diff --git a/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb new file mode 100644 index 00000000000..fddfdf851cf --- /dev/null +++ b/easybuild/easyconfigs/u/Umpire/Umpire-2024.02.1-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Umpire' +version = '2024.02.1' + +homepage = 'https://github.com/LLNL/Umpire' +description = """Umpire is a resource management library that allows the discovery, provision, +and management of memory on machines with multiple memory devices like NUMA and GPUs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/LLNL', + 'repo_name': 'Umpire', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libcamp.a', 'include/umpire/Umpire.hpp'], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..2ca769764aa --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('jax', '0.3.25', versionsuffix), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': "sed -i 's/torch>=[0-9.]*/torch/g' setup.py && ", + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb new file mode 100644 index 00000000000..d82f94349bc --- /dev/null +++ b/easybuild/easyconfigs/u/Uni-Core/Uni-Core-0.0.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Uni-Core' +version = '0.0.3' + +homepage = 'https://github.com/dptech-corp/Uni-Core' +description = "An efficient distributed PyTorch framework" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), # provides absl-py + ('tensorboardX', '2.5.1'), + ('tqdm', '4.64.0'), + ('wandb', '0.13.4'), +] + +use_pip = True + +local_preinstallopts = "sed -i -e 's/DISABLE_CUDA_EXTENSION = False/DISABLE_CUDA_EXTENSION = True/g' " +local_preinstallopts += "-e 's/torch>=[0-9.]*/torch/g' setup.py && " + +exts_list = [ + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('huggingface-hub', '0.17.3', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('tokenizers', '0.19.1', { + 'sources': ['tokenizers-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl'], + 'checksums': ['8b01afb7193d47439f091cd8f070a1ced347ad0f9144952a30a41836902fe09e'], + }), + (name, version, { + 'source_urls': ['https://github.com/dptech-corp/Uni-Core/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['e7a1e938d7d340d7aa483a05ed5ecf715bfa22f5f32a92e46d096da5b9a08043'], + 'preinstallopts': local_preinstallopts, + 'modulename': 'unicore', + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7e5cec281f2 --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.12-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.12' + +homepage = "https://www.unixodbc.org" +description = """unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.unixodbc.org/'] +checksums = ['f210501445ce21bf607ba51ef8c125e10e22dffdffec377646462df5f01915ec'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': [ + 'lib/libodbc.%s' % SHLIB_EXT, + 'lib/libodbccr.%s' % SHLIB_EXT, + 'lib/libodbcinst.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb new file mode 100644 index 00000000000..3a3c79f3875 --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.3' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'}, + {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('zstd', '1.5.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..14ed6e6d975 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.28.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.28.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb new file mode 100644 index 00000000000..5c6c6f7a122 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb @@ -0,0 +1,98 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +# Update: Pavel Tománek (Inuits) +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.2.6' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'}, + {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('XZ', '5.4.2'), + ('libGLU', '9.0.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python3 " +configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb index 9278837da13..740fd888dfb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023a.eb @@ -2,6 +2,7 @@ # Authors:: # * Fotis Georgatos # * Robert Mijakovic +# Update: Pavel Tománek (Inuits) ## easyblock = 'CMakeNinja' @@ -42,6 +43,7 @@ dependencies = [ ('XZ', '5.4.2'), ('libGLU', '9.0.3'), ('X11', '20230603'), + ('Qt5', '5.15.10'), ] separate_build_dir = True @@ -57,7 +59,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb index 8a0452f863f..3be42a90bac 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.0-foss-2023b.eb @@ -42,6 +42,7 @@ dependencies = [ ('XZ', '5.4.4'), ('libGLU', '9.0.3'), ('X11', '20231019'), + ('Qt5', '5.15.13'), ] separate_build_dir = True @@ -57,7 +58,11 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so " # Other configopts += "-DVTK_USE_MPI=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " +configopts += "-DVTK_QT_VERSION=5 " +configopts += "-DQt5_DIR=$EBROOTQT5 " +configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES " +configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES" preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index 0938ca5f98f..8f1db4ac725 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index bd9fed83da9..50053de3925 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15214/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb index 09f9e6b6120..1390fece377 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update5.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15703/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/15703/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['7b2124123347bbb593d1b8f8cf858d88829a05605769cba5c39444b0aa545473'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb index b4c024b03be..ab1cb7c1ebc 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2020_update3.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = SYSTEM -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17095/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/tec/17095/'] sources = [{'download_filename': 'vtune_profiler_2020.tar.gz', 'filename': 'vtune_profiler_%(version)s.tar.gz'}] checksums = ['b22dd61d3931ca6ab7d96df2cf8648e5e1061ab2db13b8d42e3c87586b07c974'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb index 9b6582a6610..d33e54a7818 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18012/'] sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb index cd2356a18bb..b0f65557f62 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18302/'] sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh'] checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb index e205471e1e5..16f445c0f64 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18406/'] sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb index 773718fc442..458b8143c02 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18602/'] sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh'] checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb index b8a718b77b0..e2fea76fc3a 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb @@ -13,7 +13,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/18656/'] sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh'] checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6'] diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..72cd90736a4 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1.1-GCC-13.3.0.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 +# updated by Paul Melis 2022-10-07, 2023-08-18 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.1.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['79c0d76993814d9ed9fdc29908de1cc6da08f41931bc8363084fdfae03f53ce8'] +patches = [] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Mesa', '24.1.3'), + ('libGLU', '9.0.3'), + ('pocl', '6.0'), + ('X11', '20240607'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb new file mode 100644 index 00000000000..406d78fa312 --- /dev/null +++ b/easybuild/easyconfigs/v/Visit/Visit-3.4.1-foss-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'Visit' +version = '3.4.1' + +homepage = 'https://github.com/visit-dav/visit' +description = """ +VisIt is an Open Source, interactive, scalable, visualization, animation +and analysis tool. From Unix, Windows or Mac workstations, users can +interactively visualize and analyze data ranging in scale from small +(<101 core) desktop-sized projects to large (>105 core) leadership-class +computing facility simulation campaigns. Users can quickly generate +visualizations, animate them through time, manipulate them with a +variety of operators and mathematical expressions, and save the +resulting images and animations for presentations. VisIt contains a rich +set of visualization features to enable users to view a wide variety of +data including scalar and vector fields defined on two- and +three-dimensional (2D and 3D) structured, adaptive and unstructured +meshes. Owing to its customizeable plugin design, VisIt is capabable of +visualizing data from over 120 different scientific data formats. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/visit-dav/visit/releases/download/v%(version)s/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +checksums = ['942108cb294f4c9584a1628225b0be39c114c7e9e01805fb335d9c0b507689f5'] + +builddependencies = [('CMake', '3.26.3')] +dependencies = [ + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libglvnd', '1.6.0'), + ('Qt5', '5.15.10'), + ('Qwt', '6.3.0'), + # Visit-3.4.1 needs VTK-9.2.x (not 9.3.x) - https://github.com/visit-dav/visit/issues/19547 + ('VTK', '9.2.6'), + ('FFmpeg', '6.0'), +] + +configopts = "-DVISIT_ZLIB_DIR=$EBROOTZLIB " +configopts += "-DVISIT_VTK_DIR=$EBROOTVTK -DVISIT_VTK_VERSION=$EBVERSIONVTK " +configopts += "-DVISIT_QWT_DIR=$EBROOTQWT " +configopts += "-DVISIT_QT_VERSION=$EBVERSIONQT5 -DVISIT_QT_DIR=$EBROOTQT5 " +configopts += "-DVISIT_OSMESA_DIR=$EBROOTMESA " +configopts += "-DVISIT_MESAGL_DIR=$EBROOTLIBGLVND " +configopts += "-DPYTHON_DIR=$EBROOTPYTHON " +configopts += "-DVISIT_PYTHON_SKIP_INSTALL=ON " +configopts += "-DVISIT_PARALLEL=ON -DVISIT_MPI_COMPILER=$MPICC -DVISIT_MPI_COMPILER_CXX=$MPICXX " +configopts += "-DOpenGL_GL_PREFERENCE=GLVND " + +# add missing include to fix make step +prebuildopts = "sed -i '23 a #include ' %(builddir)s/%(namelower)s%(version)s/src/gui/QvisStripChart.C && " + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['frontendlauncher', 'frontendlauncher.py', 'visit']], + 'dirs': ['%(version)s/bin'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..ab4e77dea46 --- /dev/null +++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'versioningit' +version = '3.1.2' + +homepage = 'https://github.com/jwodder/versioningit' +description = """versioningit is yet another Python packaging plugin for automatically determining your +package’s version based on your version control repository’s tags. +Unlike others, it allows easy customization of the version format and even lets you easily override +the separate functions used for version extraction & calculation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('hatchling', '1.24.2'), +] +dependencies = [('Python', '3.12.3')] + +sources = [SOURCE_TAR_GZ] +checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 122f3d8d6c8..c36c435d1da 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.6', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb index a0b9921fb5c..2820042ba9d 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.11.5'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.7', { diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb index 9c6a84c5304..65f1ced6cae 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.26.2-GCCcore-13.3.0.eb @@ -18,11 +18,8 @@ dependencies = [ ('Python', '3.12.3'), ] -exts_default_options = { - 'download_dep_fail': True, - 'sanity_pip_check': True, - 'use_pip': True, -} +sanity_pip_check = True +use_pip = True exts_list = [ ('distlib', '0.3.8', { diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index a8881dbe118..0dd0b641ceb 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -61,6 +61,10 @@ fix_perl_shebang_for = [ 'bashtime2csh.pl_lapw', ] +# skip running of serial/parallel benchmark, because links to download test_case.tar.gz and mpi-benchmark.tar.gz +# from http://www.wien2k.at/reg_user/benchmark/ that are used by WIEN2k easyblock are broken... +runtest = False + tests = [ # test case 1: NaCl ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..53a2aa183b1 --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20231117-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20231117' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'checksums': ['7af424181436f1800cc0b7d75cf40ede34e9ddf1ba4983a910832fcf4aade4a4'], + 'modulename': 'whisper', + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb new file mode 100644 index 00000000000..f3b254591f5 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2023a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb new file mode 100644 index 00000000000..010b73f371b --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.6.0'), + ('Cartopy', '0.20.3'), + ('dask', '2022.10.0'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.12.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['0337b4a0798ded019b26e0746b7b7baeb6f21344a2a2e3704965049972ccbf51'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e2b625d10bc9b3ea2f33356fe467683b474c0a5410ff10ea6a708238d9172a10'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb new file mode 100644 index 00000000000..d53e56422bc --- /dev/null +++ b/easybuild/easyconfigs/w/wradlib/wradlib-2.0.3-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'wradlib' +version = '2.0.3' + +homepage = 'https://docs.wradlib.org/' +description = """ +The wradlib project has been initiated in order to facilitate the use of weather +radar data as well as to provide a common platform for research on new +algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('xarray', '2023.9.0'), + ('Cartopy', '0.22.0'), + ('dask', '2023.9.2'), + ('matplotlib', '3.7.2'), + ('netcdf4-python', '1.6.4'), + ('h5netcdf', '1.2.0'), + ('geopandas', '0.14.2'), +] + +use_pip = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('cmweather', '0.3.2', { + 'checksums': ['d374b068fcbfeed87bc511f1f77a6047ae752f4a175a852587414b615b4baa5a'], + }), + ('lat_lon_parser', '1.3.0', { + 'checksums': ['e3a65dacd5b25a18c56e3ae31b11cd724480be7fe8db2df1c46ed0dd322a1fca'], + }), + ('xarray-datatree', '0.0.13', { + 'modulename': 'datatree', + 'checksums': ['f42bd519cab8754eb8a98749464846893b59560318520c45212e85c46af692c9'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('xradar', '0.5.1', { + 'checksums': ['b71021164b005f3270afd2079b8ed831a01ed43accbb7fc42c79e31a342546c5'], + }), + (name, version, { + 'checksums': ['0d5448a1dd0e030bdd36f7bbc69fa50aee7fb74dbc7b6407d2dc52d18ea40c49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb new file mode 100644 index 00000000000..91e9be0529c --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-2.1.1-gfbf-2023b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '2.1.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4b1729837f9f1ba88a32ef1be3f8efb860fee6454a68719b196dc88032c23d97'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1d4cbe24543 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.3.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0210' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('Perl', '5.38.2'), + ('Perl-bundle-CPAN', '5.38.2'), + ('libxml2', '2.12.7'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.83', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a2a4cccf421 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20240513-GCCcore-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20240513' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/31e19f92/'] +sources = [{'download_filename': '%(name)s-4613ac3c.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['cf7e66bd0a75f3baba3502b58c80ee388b3d80a9a01be806337dd2214b8a290e'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('NASM', '2.16.03'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fc9ad81c0cb --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.6-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.6' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['663531f341c5389f460d730e62e10a4fcca3428ca2ca109693867bc5fe2e2807'] + +builddependencies = [ + ('binutils', '2.42'), + ('CMake', '3.29.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1 -DENABLE_PIC=ON' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb new file mode 100644 index 00000000000..c8454e53dbb --- /dev/null +++ b/easybuild/easyconfigs/x/xskillscore/xskillscore-0.0.26-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'xskillscore' +version = '0.0.26' + +homepage = 'https://xskillscore.readthedocs.io' +description = """ +xskillscore is an open source project and Python package that provides verification metrics of +deterministic (and probabilistic from properscoring) forecasts with xarray. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('dask', '2023.9.2'), + ('SciPy-bundle', '2023.07'), + ('statsmodels', '0.14.1'), + ('xarray', '2023.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('properscoring', '0.1', { + 'checksums': ['b0cc4963cc218b728d6c5f77b3259c8f835ae00e32e82678cdf6936049b93961'], + }), + ('xhistogram', '0.3.2', { + 'checksums': ['56b0751e1469eaed81710f644c8ba5c574b51883baa2feee26a95f2f708f91a1'], + }), + (name, version, { + 'checksums': ['780a424c1ab3eedf526a45ba8e6cf6dca61b17339252115a4e25ea8c5833ada5'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb index 97ce290bfe0..81ee768fed0 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0-gfbf-2023a.eb @@ -11,7 +11,13 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'] +patches = [ + 'xtb-6.7.0_fix-tblite-pr1072.patch' +] +checksums = [ + {'xtb-6.7.0.tar.gz': '9cf1997064d2d5bde7fae4cec6f873469602e6554872ad79de4079f022855ae2'}, + {'xtb-6.7.0_fix-tblite-pr1072.patch': 'cb8de869fc4a7c6bde44c61a479fc9edb3ccdc47c2a71f15ef124326f8a117e6'}, +] builddependencies = [ ('Meson', '1.1.1'), diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..74e2ea4950e --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.0_fix-tblite-pr1072.patch @@ -0,0 +1,487 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff -Naur xtb-6.7.0.orig/src/dipro/xtb.F90 xtb-6.7.0/src/dipro/xtb.F90 +--- xtb-6.7.0.orig/src/dipro/xtb.F90 2024-08-23 13:50:09.000345982 +0200 ++++ xtb-6.7.0/src/dipro/xtb.F90 2024-08-23 14:14:49.499145489 +0200 +@@ -50,11 +50,11 @@ + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff -Naur xtb-6.7.0.orig/src/dipro.F90 xtb-6.7.0/src/dipro.F90 +--- xtb-6.7.0.orig/src/dipro.F90 2024-08-23 13:50:08.996896000 +0200 ++++ xtb-6.7.0/src/dipro.F90 2024-08-23 13:55:44.571958738 +0200 +@@ -130,6 +130,10 @@ + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff -Naur xtb-6.7.0.orig/src/tblite/calculator.F90 xtb-6.7.0/src/tblite/calculator.F90 +--- xtb-6.7.0.orig/src/tblite/calculator.F90 2024-08-23 13:50:09.192101000 +0200 ++++ xtb-6.7.0/src/tblite/calculator.F90 2024-08-23 14:18:13.034251635 +0200 +@@ -144,11 +144,11 @@ + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +diff -Naur xtb-6.7.0.orig/subprojects/mstore.wrap xtb-6.7.0/subprojects/mstore.wrap +--- xtb-6.7.0.orig/subprojects/mstore.wrap 2024-08-23 13:50:09.235197230 +0200 ++++ xtb-6.7.0/subprojects/mstore.wrap 2024-08-23 14:18:50.314014066 +0200 +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff -Naur xtb-6.7.0.orig/test/unit/test_ptb.F90 xtb-6.7.0/test/unit/test_ptb.F90 +--- xtb-6.7.0.orig/test/unit/test_ptb.F90 2024-08-23 13:50:09.260760000 +0200 ++++ xtb-6.7.0/test/unit/test_ptb.F90 2024-08-23 14:34:18.302090669 +0200 +@@ -186,12 +186,37 @@ + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -670,10 +799,10 @@ + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +837,37 @@ + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +925,9 @@ + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1113,35 @@ + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1225,36 @@ + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1274,7 @@ + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb new file mode 100644 index 00000000000..09d459d356b --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1-gfbf-2023b.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.7.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'xtb-6.7.1_fix-tblite-pr1072.patch', + 'xtb-6.7.1_fix-dftd4-test.patch', +] +checksums = [ + {'xtb-6.7.1.tar.gz': '52506a689147cdb4695bf1c666158b6d6d6b31726fecaa5bf53af7f4e3f3d20d'}, + {'xtb-6.7.1_fix-tblite-pr1072.patch': '1f10fef3e94c29926b1f632acc94c3ec92be861ee5c5139104194172726ffe68'}, + {'xtb-6.7.1_fix-dftd4-test.patch': '340e7d5cbc6bbaf0c53d4d292f3624cd67455b7a817818fe2cc8d26f5c34864b'}, +] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +configopts = "-Dlapack='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +pretestopts = 'export OMP_NUM_THREADS=2 && ' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch new file mode 100644 index 00000000000..0405b372a8a --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-dftd4-test.patch @@ -0,0 +1,20 @@ +fix for failing xtb test: + 72/148 dftd4 / param FAIL 1.85s exit status 1 + +from meson-logs/testlog.txt: +# Testing: param + Starting rational-damping ... (1/1) + ... rational-damping [FAILED] + Message: Condition not fullfilled + +see https://github.com/grimme-lab/xtb/pull/1085 +diff --git a/subprojects/dftd4.wrap b/subprojects/dftd4.wrap +index 46dc07ad9..e3e93f459 100644 +--- a/subprojects/dftd4.wrap ++++ b/subprojects/dftd4.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = dftd4 + url = https://github.com/dftd4/dftd4 +-revision = v3.5.0 ++revision = v3.6.0 diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch new file mode 100644 index 00000000000..0684569d3e4 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.7.1_fix-tblite-pr1072.patch @@ -0,0 +1,528 @@ +see https://github.com/grimme-lab/xtb/pull/1072 + https://github.com/grimme-lab/xtb/issues/1091 +diff --git a/src/dipro.F90 b/src/dipro.F90 +index 42a136364..ab64e0710 100644 +--- a/src/dipro.F90 ++++ b/src/dipro.F90 +@@ -130,6 +130,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + !=========================set up calculator=========================================== + + call get_calculator(xcalc, struc, tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + call new_wavefunction(wfn, struc%nat, xcalc%bas%nsh, xcalc%bas%nao, & + & 1, set%etemp * ktoau) + wfn%nspin=1 +@@ -258,6 +262,10 @@ subroutine get_jab(env, tblite, mol, fragment, dipro) + write(*,'(A,I2)') "unpaired e- of fragment : ", mfrag(ifr)%uhf + + call get_calculator(fcalc(ifr), mfrag(ifr), tblite%method, error) ++ if (allocated(error)) then ++ call env%error(error%message, source) ++ return ++ end if + !> mol%charge is updated automatically from wfn by tblite library + call new_wavefunction(wfx(ifr), mfrag(ifr)%nat, fcalc(ifr)%bas%nsh, fcalc(ifr)%bas%nao, & + & 1, set%etemp * ktoau) +diff --git a/src/dipro/xtb.F90 b/src/dipro/xtb.F90 +index 95aff7848..4db948a3e 100644 +--- a/src/dipro/xtb.F90 ++++ b/src/dipro/xtb.F90 +@@ -50,11 +50,11 @@ subroutine get_calculator(xcalc, mol, method, error) + call fatal_error(error, "Unknown method '"//method//"' requested") + ! error stop + case("gfn2") +- call new_gfn2_calculator(xcalc, mol) ++ call new_gfn2_calculator(xcalc, mol, error) + case("gfn1") +- call new_gfn1_calculator(xcalc, mol) ++ call new_gfn1_calculator(xcalc, mol, error) + case("ipea1") +- call new_ipea1_calculator(xcalc, mol) ++ call new_ipea1_calculator(xcalc, mol, error) + end select + end subroutine get_calculator + #endif +diff --git a/src/tblite/calculator.F90 b/src/tblite/calculator.F90 +index 653e6b285..f05087414 100644 +--- a/src/tblite/calculator.F90 ++++ b/src/tblite/calculator.F90 +@@ -150,16 +150,16 @@ subroutine newTBLiteCalculator(env, mol, calc, input) + case default + call fatal_error(error, "Unknown method '"//method//"' requested") + case("gfn2") +- call new_gfn2_calculator(calc%tblite, struc) ++ call new_gfn2_calculator(calc%tblite, struc, error) + case("gfn1") +- call new_gfn1_calculator(calc%tblite, struc) ++ call new_gfn1_calculator(calc%tblite, struc, error) + case("ipea1") +- call new_ipea1_calculator(calc%tblite, struc) ++ call new_ipea1_calculator(calc%tblite, struc, error) + case("ceh") + calc%guess = method + calc%nspin = 1 +- calc%etemp = 5000.0_wp * kt +- call new_ceh_calculator(calc%tblite, struc) ++ calc%etemp = 4000.0_wp * kt ++ call new_ceh_calculator(calc%tblite, struc, error) + end select + end if + if (allocated(error)) then +@@ -244,18 +244,18 @@ subroutine newTBLiteWavefunction(env, mol, calc, chk) + block + use tblite_context, only : context_type, context_terminal + use tblite_context_terminal, only : escape +- use tblite_ceh_singlepoint, only : ceh_guess ++ use tblite_ceh_singlepoint, only : ceh_singlepoint + use tblite_lapack_solver, only : lapack_solver + use tblite_lapack_solver, only : lapack_algorithm + type(context_type) :: ctx +- ++ + ctx%solver = lapack_solver(lapack_algorithm%gvd) + ctx%terminal = context_terminal(calc%color) + + write (env%unit, '(1x,a)') escape(ctx%terminal%cyan) // "Calculation of CEH charges" // & + & escape(ctx%terminal%reset) +- +- call ceh_guess(ctx, calc%tblite, struc, error, wfn, calc%accuracy, 1) ++ ++ call ceh_singlepoint(ctx, calc%tblite, struc, wfn, calc%accuracy, 1) + end block + end select + end associate +diff --git a/subprojects/mstore.wrap b/subprojects/mstore.wrap +index acf5df9de..0dfe716c0 100644 +--- a/subprojects/mstore.wrap ++++ b/subprojects/mstore.wrap +@@ -1,4 +1,4 @@ + [wrap-git] + directory = mstore + url = https://github.com/grimme-lab/mstore +-revision = v0.2.0 ++revision = v0.3.0 +diff --git a/test/unit/test_ptb.F90 b/test/unit/test_ptb.F90 +index 16c14cbe4..5e585f90d 100644 +--- a/test/unit/test_ptb.F90 ++++ b/test/unit/test_ptb.F90 +@@ -186,12 +186,37 @@ subroutine test_ptb_overlap(error) + !> (Scaled) overlap matrix + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.93209460_wp, & ! 1,2 +- & 0.35489609_wp, & ! 1,3 +- & 0.65682608_wp, & ! 2,3 +- & 0.05627743_wp, & ! 1,15 +- & -0.14217162_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.41844087_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.93209460_wp, & ! s(Mg)-s(Mg) ++ & 0.35489609_wp, & ! s(Mg)-s(Mg) ++ & 0.65682608_wp, & ! s(Mg)-s(Mg) ++ & 0.05627743_wp, & ! s(Mg)-s(H) ++ & -0.14217162_wp, & ! s(Mg)-pz(H) ++ & 0.41844087_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -215,7 +240,7 @@ subroutine test_ptb_overlap(error) + call check_(error, ints%overlap(2, 3), overlap_exp(3), thr=thr) + call check_(error, ints%overlap(1, 15), overlap_exp(4), thr=thr) + call check_(error, ints%overlap(1, 23), overlap_exp(5), thr=thr) +- call check_(error, ints%overlap(12, 22), overlap_exp(6), thr=thr) ++ call check_(error, ints%overlap(11, 22), overlap_exp(6), thr=thr) + + end subroutine test_ptb_overlap + +@@ -249,12 +274,37 @@ subroutine test_ptb_overlap_h0(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: overlap_exp(6) = [ & +- & 0.95689468_wp, & ! 1,2 +- & 0.39195790_wp, & ! 1,3 +- & 0.62961212_wp, & ! 2,3 +- & 0.03782850_wp, & ! 1,15 +- &-0.13826216_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.43334922_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.95689468_wp, & ! s(Mg)-s(Mg) ++ & 0.39195790_wp, & ! s(Mg)-s(Mg) ++ & 0.62961212_wp, & ! s(Mg)-s(Mg) ++ & 0.03782850_wp, & ! s(Mg)-s(H) ++ &-0.13826216_wp, & ! s(Mg)-pz(H) ++ & 0.43334922_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -286,7 +336,7 @@ subroutine test_ptb_overlap_h0(error) + & message=message) + call check_(error, auxints%overlap_h0_1(1, 23), overlap_exp(5), thr=thr, & + & message=message) +- call check_(error, auxints%overlap_h0_1(12, 22), overlap_exp(6), thr=thr, & ++ call check_(error, auxints%overlap_h0_1(11, 22), overlap_exp(6), thr=thr, & + & message=message) + + end subroutine test_ptb_overlap_h0 +@@ -319,12 +369,37 @@ subroutine test_ptb_overlap_SX(error) + real(wp), allocatable :: overlap_sx(:, :), overlap_oneminusx(:, :) + character(len=:), allocatable :: message + real(wp), parameter :: overlap_oneminusx_exp(6) = [ & +- & 0.70788_wp, & ! 1,2 +- & 0.16203_wp, & ! 1,3 +- & 0.41532_wp, & ! 2,3 +- & 0.01449_wp, & ! 1,15 +- &-0.07203_wp, & ! 1,24; diffferent because of tblite ordering +- & 0.28751_wp] ! 14,23; diffferent because of tblite ordering ++ & 0.70788_wp, & ! s(Mg)-s(Mg) ++ & 0.16203_wp, & ! s(Mg)-s(Mg) ++ & 0.41532_wp, & ! s(Mg)-s(Mg) ++ & 0.01449_wp, & ! s(Mg)-s(H) ++ &-0.07203_wp, & ! s(Mg)-pz(H) ++ & 0.28751_wp] ! dyz(Mg)-py(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -356,7 +431,7 @@ subroutine test_ptb_overlap_SX(error) + & message=message) + call check_(error, overlap_oneminusx(1, 23), overlap_oneminusx_exp(5), thr=thr2, & + & message=message) +- call check_(error, overlap_oneminusx(12, 22), overlap_oneminusx_exp(6), thr=thr2, & ++ call check_(error, overlap_oneminusx(11, 22), overlap_oneminusx_exp(6), thr=thr2, & + & message=message) + + end subroutine test_ptb_overlap_SX +@@ -392,10 +467,37 @@ subroutine test_ptb_V_ECP(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: vecp_ref(4) = [ & +- & 0.077719_wp, & ! 1,1 ; diffferent because of tblite ordering +- & -0.059122_wp, & ! 1,3 ; diffferent because of tblite ordering +- & 0.052775_wp, & ! 3,5 ; diffferent because of tblite ordering +- & 0.117176_wp] ! 9,9 ; diffferent because of tblite ordering ++ & 0.077719_wp, & ! s(B)-s(B) ++ & -0.059122_wp, & ! s(B)-px(B) ++ & 0.052775_wp, & ! px(B)-px(B) ++ & 0.117176_wp] ! dx2-y2(B)-dx2-y2(B) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -434,7 +536,7 @@ subroutine test_ptb_V_ECP(error) + & message=message) + call check_(error, vecp(5, 8), vecp_ref(3), thr=thr2, & + & message=message) +- call check_(error, vecp(12, 12), vecp_ref(4), thr=thr2, & ++ call check_(error, vecp(13, 13), vecp_ref(4), thr=thr2, & + & message=message) + end subroutine test_ptb_V_ECP + +@@ -629,12 +731,39 @@ subroutine test_ptb_hamiltonian_h0(error) + real(wp), allocatable :: vecp(:, :) + + real(wp), parameter :: h0_ref(6) = [ & +- & -1.59330281_wp, & ! 1,1 +- & -2.24996207_wp, & ! 1,2 +- & 0.34974782_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.0_wp, & ! 7,11 ; different because of tblite ordering +- & -1.17757007_wp, & ! 3,6 ; different because of tblite ordering +- & 0.48301561_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -1.59330281_wp, & ! s(B)-s(B) ++ & -2.24996207_wp, & ! s(B)-s(B) ++ & 0.34974782_wp, & ! s(B)-py(Cl) ++ & 0.0_wp, & ! dx2-y2(B)-py(B) ++ & -1.17757007_wp, & ! px(B)-px(B) ++ & 0.48301561_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: levels(10) = [ & + & -0.796651404_wp, & + & -0.269771638_wp, & +@@ -665,15 +794,16 @@ subroutine test_ptb_hamiltonian_h0(error) + & alpha_scal=id_to_atom(mol, ptbData%hamiltonian%kalphah0l)) + allocate (vecp(bas%nao, bas%nao), source=0.0_wp) + ++ ints%hamiltonian = 0.0_wp + call get_hamiltonian(mol, list, bas, ptbData%hamiltonian, ptbData%hamiltonian%kla, auxints%overlap_h0_1, & + & levels, ints%hamiltonian, ptbGlobals%kpol, ptbGlobals%kitr, ptbGlobals%kitocod) + message = "H0 matrix element not matching to expected value." + call check_(error, ints%hamiltonian(1, 1), h0_ref(1), thr=thr) + call check_(error, ints%hamiltonian(1, 2), h0_ref(2), thr=thr) +- call check_(error, ints%hamiltonian(1, 22), h0_ref(3), thr=thr) ++ call check_(error, ints%hamiltonian(1, 24), h0_ref(3), thr=thr) + call check_(error, ints%hamiltonian(13, 6), h0_ref(4), thr=thr) + call check_(error, ints%hamiltonian(8, 5), h0_ref(5), thr=thr) +- call check_(error, ints%hamiltonian(13, 26), h0_ref(6), thr=thr) ++ call check_(error, ints%hamiltonian(9, 22), h0_ref(6), thr=thr) + end subroutine test_ptb_hamiltonian_h0 + + subroutine test_ptb_V_XC(error) +@@ -708,10 +838,37 @@ subroutine test_ptb_V_XC(error) + type(error_type), allocatable, intent(out) :: error + character(len=:), allocatable :: message + real(wp), parameter :: Vxc_ref(4) = [ & +- & -0.92793357_wp, & ! 1,1 +- & -0.85981333_wp, & ! 1,2 +- & 0.06632750_wp, & ! 1,23 ; diffferent because of tblite ordering +- & 0.00151880_wp] ! 11,24 ; diffferent because of tblite ordering ++ & -0.92793357_wp, & ! s(B)-s(B) ++ & -0.85981333_wp, & ! s(B)-s(B) ++ & 0.06632750_wp, & ! s(B)-dz2(Cl) ++ & 0.00151880_wp] ! dxy(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) ++ + real(wp), parameter :: xyz(3, 2) = reshape([ & + & 2.0_wp, 0.0_wp, 0.0_wp, & + & 0.0_wp, 0.0_wp, 0.0_wp], [3, 2]) +@@ -769,9 +926,9 @@ subroutine test_ptb_V_XC(error) + & message=message) + call check_(error, Vxc(1, 2), Vxc_ref(2), thr=thr, & + & message=message) +- call check_(error, Vxc(1, 22), Vxc_ref(3), thr=thr, & ++ call check_(error, Vxc(1, 24), Vxc_ref(3), thr=thr, & + & message=message) +- call check_(error, Vxc(13, 26), Vxc_ref(4), thr=thr, & ++ call check_(error, Vxc(9, 22), Vxc_ref(4), thr=thr, & + & message=message) + + end subroutine test_ptb_V_XC +@@ -957,10 +1114,35 @@ subroutine test_ptb_coulomb_potential(error) + !> Conversion factor from temperature to energy + real(wp), parameter :: kt = 3.166808578545117e-06_wp + real(wp), parameter :: coulomb_pot_ref(4) = [ & +- & -0.05693153_wp, & ! 1,1 +- & -0.33917531_wp, & ! 1,2 +- & -0.00539212_wp, & ! 1,21 ; diffferent because of tblite ordering +- & 0.01305793_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.05693153_wp, & ! s(Mg)-s(Mg) ++ & -0.33917531_wp, & ! s(Mg)-s(Mg) ++ & -0.00539212_wp, & ! s(Mg)-s(H) ++ & 0.01305793_wp] ! pz(Mg)-pz(H) ++ ! 1: s(Mg) ++ ! 2: s(Mg) ++ ! 3: s(Mg) ++ ! 4: py(Mg) ++ ! 5: pz(Mg) ++ ! 6: px(Mg) ++ ! 7: py(Mg) ++ ! 8: pz(Mg) ++ ! 9: px(Mg) ++ ! 10: dxy(Mg) ++ ! 11: dyz(Mg) ++ ! 12: dz2(Mg) ++ ! 13: dxz(Mg) ++ ! 14: dx2-y2(Mg) ++ ! 15: s(H) ++ ! 16: s(H) ++ ! 17: py(H) ++ ! 18: pz(H) ++ ! 19: px(H) ++ ! 20: s(H) ++ ! 21: s(H) ++ ! 22: py(H) ++ ! 23: pz(H) ++ ! 24: px(H) ++ + real(wp), allocatable :: lattr(:, :) + real(wp) :: cutoff + +@@ -1044,10 +1226,36 @@ subroutine test_ptb_plus_U_potential(error) + integer, parameter :: nat = 2 + integer, parameter :: at(nat) = [5, 17] + real(wp), parameter :: plusU_pot_ref(4) = [ & +- & -0.0023185_wp, & ! 1,1 +- & -0.0018289_wp, & ! 1,2 +- & -0.5266562_wp, & ! 1,21 ; diffferent because of tblite ordering +- & -1.6745659_wp] ! 6,24 ; diffferent because of tblite ordering ++ & -0.0023185_wp, & ! s(B)-s(B) ++ & -0.0018289_wp, & ! s(B)-s(B) ++ & -0.5266562_wp, & ! s(B)-pz(Cl) ++ & -1.6745659_wp] ! px(B)-dxy(Cl) ++ ! 1: s(B) ++ ! 2: s(B) ++ ! 3: py(B) ++ ! 4: pz(B) ++ ! 5: px(B) ++ ! 6: py(B) ++ ! 7: pz(B) ++ ! 8: px(B) ++ ! 9: dxy(B) ++ ! 10: dyz(B) ++ ! 11: dz2(B) ++ ! 12: dxz(B) ++ ! 13: dx2-y2(B) ++ ! 14: s(Cl) ++ ! 15: s(Cl) ++ ! 16: py(Cl) ++ ! 17: pz(Cl) ++ ! 18: px(Cl) ++ ! 19: py(Cl) ++ ! 20: pz(Cl) ++ ! 21: px(Cl) ++ ! 22: dxy(Cl) ++ ! 23: dyz(Cl) ++ ! 24: dz2(Cl) ++ ! 25: dxz(Cl) ++ ! 26: dx2-y2(Cl) + + call new(mol, at, xyz) + allocate (ptbData) +@@ -1067,7 +1275,7 @@ subroutine test_ptb_plus_U_potential(error) + call check_(error, wfn%coeff(1, 1, 1), plusU_pot_ref(1), thr=thr) + call check_(error, wfn%coeff(1, 2, 1), plusU_pot_ref(2), thr=thr) + call check_(error, wfn%coeff(1, 20, 1), plusU_pot_ref(3), thr=thr) +- call check_(error, wfn%coeff(8, 26, 1), plusU_pot_ref(4), thr=thr) ++ call check_(error, wfn%coeff(8, 22, 1), plusU_pot_ref(4), thr=thr) + + end subroutine test_ptb_plus_U_potential + diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..2ab12a60fca --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-13.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('PyYAML', '6.0.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..5ac8fd8176f --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..48cc38e0d7c --- /dev/null +++ b/easybuild/easyconfigs/y/yell/yell-2.2.2-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'RubyGem' + +name = 'yell' +version = '2.2.2' + +homepage = 'https://github.com/rudionrails/yell' +description = """Yell - Your Extensible Logging Library is a comprehensive logging replacement for Ruby.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://rubygems.org/downloads/'] +sources = ['%(name)s-%(version)s.gem'] +checksums = ['1d166f3cc3b6dc49a59778ea7156ed6d8de794c15106d48ffd6cbb061b9b26bc'] + +gem_file = '%(name)s-%(version)s.gem' + +dependencies = [ + ('Ruby', '3.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bbf260ff417 --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-tools/yelp-tools-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MesonNinja' + +name = 'yelp-tools' +version = '42.1' + +homepage = 'https://gitlab.gnome.org/GNOME/yelp-tools' +description = """yelp-tools is a collection of scripts and build utilities to help create, +manage, and publish documentation for Yelp and the web. Most of the heavy +lifting is done by packages like yelp-xsl and itstool. This package just +wraps things up in a developer-friendly way.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-tools/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4776766816aaa4fff5a9be7229d03e2444fca2f60a11f645c6171abe8bb73925'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('yelp-xsl', '42.1'), + ('ITSTool', '2.0.7'), + ('libxml2', '2.11.4'), + ('mallard-ducktype', '1.0.2'), + ('lxml', '4.9.2'), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': [ + 'bin/yelp-build', + 'bin/yelp-check', + 'bin/yelp-new', + ], + 'dirs': ['share/%(name)s'], +} + +sanity_check_commands = [ + 'yelp-build cache -h', + 'yelp-check hrefs -h', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ad7d8eddb4e --- /dev/null +++ b/easybuild/easyconfigs/y/yelp-xsl/yelp-xsl-42.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'yelp-xsl' +version = '42.1' + +homepage = "https://gitlab.gnome.org/GNOME/yelp-xslg" +description = """yelp-xsl is a collection of programs and data files to help you build, maintain, + and distribute documentation. It provides XSLT stylesheets that can be built upon for help + viewers and publishing systems. These stylesheets output JavaScript and CSS content, + and reference images provided by yelp-xsl. This package also redistributes copies + of the jQuery and jQuery.Syntax JavaScript libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/yelp-xsl/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['00f3ee8d9fa048d80063cc09477d24a09349e35c58ffdf9ecea253a4ca882068'] + +builddependencies = [ + ('binutils', '2.40'), + ('ITSTool', '2.0.7'), + ('gettext', '0.21.1'), + ('Autotools', '20220317'), +] + +preconfigopts = 'NOCONFIGURE=1 ./autogen.sh && ' + +sanity_check_paths = { + 'files': [], + 'dirs': [ + 'share/pkgconfig', + 'share/%(name)s', + ] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..a925168f147 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.0' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] +dependencies = [ + ('Python', '3.12.3'), + ('GMP', '6.3.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..98db227b9aa --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.5' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.20'), + ('util-linux', '2.40'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb new file mode 100644 index 00000000000..57432d0e0ce --- /dev/null +++ b/easybuild/easyconfigs/z/Zoltan/Zoltan-3.901-foss-2023a.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'Zoltan' +version = '3.901' + +homepage = "https://sandialabs.github.io/Zoltan/" +description = """Zoltan Dynamic Load Balancing and Graph Algorithm Toolkit""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +github_account = 'sandialabs' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030c22d9f7532d3076e40cba1f03a63b2ee961d8cc9a35149af4a3684922a910'] + +dependencies = [ + ('gzip', '1.12'), + ('SCOTCH', '7.0.3'), + ('ParMETIS', '4.0.3'), +] + +preconfigopts = 'mkdir build && cd build &&' +configure_cmd = '../configure' +configopts = ' '.join([ + '--enable-gzip', + '--with-scotch', + '--with-scotch-incdir=$EBROOTSCOTCH/include', + '--with-scotch-libdir=$EBROOTSCOTCH/lib', + '--with-parmetis', + '--with-parmetis-incdir=$EBROOTPARMETIS/include', + '--with-parmetis-libdir=$EBROOTPARMETIS/lib', + '--disable-examples', + '--disable-tests', +]) +prebuildopts = 'cd build &&' +buildopts = 'everything' +preinstallopts = 'cd build &&' + +sanity_check_paths = { + 'files': ['lib/libzoltan.a', 'include/zoltan.h'], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..266b927072a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'zlib-ng' +version = '2.2.1' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('versioningit', '3.1.2'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['ec6a76169d4214e2e8b737e0850ba4acb806c69eeace6240ed4481b9f5c57cdf'], + 'start_dir': '%(name)s-%(version)s', + 'configopts': '-DZLIB_ENABLE_TESTS=ON', + }), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, '0.5.0', { + 'source_tmpl': 'zlib_ng-%(version)s.tar.gz', + 'checksums': ['3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2'], + 'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true', + 'modulename': 'zlib_ng', + }), +] + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb new file mode 100644 index 00000000000..187f8da34f7 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3.1-GCCcore-14.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3.1' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '14.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.42', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 8d3cd7f76d0..15cbcf7470d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.3.dev0' +VERSION = '4.9.5.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d228333cca6..74f98af5cf8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -663,6 +663,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15 'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])], + # Visit-3.4.1 requires VTK 9.2.x + 'VTK': [('9.2.6;', ['Visit-3.4.1-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 @@ -999,14 +1001,13 @@ def test_easyconfig_locations(self): # ignore git/svn dirs & archived easyconfigs if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + # check whether list of .eb files is non-empty, only exception: TEMPLATE.eb + easyconfig_files = [fn for fn in filenames if fn.endswith('eb') and fn != 'TEMPLATE.eb'] if easyconfig_files: # check whether path matches required pattern if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + if not dirpath.endswith('/easybuild/easyconfigs'): + self.fail("There should be no easyconfig files in %s, found %s" % (dirpath, easyconfig_files)) def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" @@ -1027,7 +1028,7 @@ def test_easyconfig_name_clashes(self): duplicates[name] = names[name] if duplicates: - self.assertTrue(False, "EasyConfigs with case-insensitive name clash: %s" % duplicates) + self.fail("EasyConfigs with case-insensitive name clash: %s" % duplicates) @skip_if_not_pr_to_non_main_branch() def test_pr_sha256_checksums(self): @@ -1045,25 +1046,19 @@ def test_pr_sha256_checksums(self): 'R-bundle-Bioconductor-3.[2-5]', ] - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - bundle_easyblocks = ['Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] - for ec in self.changed_ecs: - if ec['easyblock'] in bundle_easyblocks or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + retained_changed_ecs = [ec for ec in self.changed_ecs if not ec['deprecated']] + + # The check_sha256_checksums function creates an EasyBlock instance. + # For easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__. + # Therefore, we need to a operate on a copy of those easyconfigs. + bundle_easyblocks = {'Bundle', 'CargoPythonBundle', 'PythonBundle', 'EB_OpenSSL_wrapper'} + + def is_bundle(ec): + return ec['easyblock'] in bundle_easyblocks or ec['name'] == 'Clang-AOMP' + ecs = [ec.copy() if is_bundle(ec) else ec for ec in retained_changed_ecs] + checksum_issues = check_sha256_checksums(ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() @@ -1084,6 +1079,11 @@ def test_pr_python_packages(self): r'.*-2016[ab]-Python-.*', # mympirun is installed with system Python, pip may not be installed for system Python r'vsc-mympirun.*', + # ReFrame intentionally installs its deps in a %(installdir)s/external subdir, which is added + # to sys.path by the ReFrame command, and is intentionally NOT on the PYTHONPATH. + # Thus, a pip check fails, but this is expected and ok, it is still a working ReFrame installation + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/21269 for more info + r'ReFrame.*', ] failing_checks = [] @@ -1459,6 +1459,9 @@ def template_easyconfig_test(self, spec): ] failing_checks.extend("Old URL '%s' found" % old_url for old_url in old_urls if old_url in ec.rawtxt) + # Note the use of app.cfg which might contain sources populated by e.g. the Cargo easyblock + sources, patches, checksums = app.cfg['sources'], app.cfg['patches'], app.cfg['checksums'] + # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # easyblocks without a build step @@ -1475,7 +1478,7 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + requires_binutils &= bool(sources or ec['exts_list'] or ec.get('components')) if requires_binutils: # dependencies() returns both build and runtime dependencies @@ -1506,13 +1509,13 @@ def template_easyconfig_test(self, spec): if openssl_osdep: failing_checks.append("OpenSSL should not be listed as OS dependency") - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] + src_cnt = len(sources) + patch_checksums = checksums[src_cnt:] # make sure all patch files are available specdir = os.path.dirname(spec) basedir = os.path.dirname(os.path.dirname(specdir)) - for idx, patch in enumerate(ec['patches']): + for idx, patch in enumerate(patches): patch_dir = specdir if isinstance(patch, str): patch_name = patch @@ -1535,7 +1538,7 @@ def template_easyconfig_test(self, spec): # make sure 'source' step is not being skipped, # since that implies not verifying the checksum - if ec['checksums'] and ('source' in ec['skipsteps']): + if checksums and ('source' in ec['skipsteps']): failing_checks.append("'source' step should not be skipped, since that implies not verifying checksums") for ext in ec.get_ref('exts_list'):