Skip to content

Commit

Permalink
Merge pull request #15212 from easybuilders/4.5.x
Browse files Browse the repository at this point in the history
release EasyBuild v4.5.4
  • Loading branch information
SebastianAchilles authored Mar 31, 2022
2 parents 3c7ef04 + 933ebd3 commit 478fa1d
Show file tree
Hide file tree
Showing 302 changed files with 10,209 additions and 333 deletions.
61 changes: 60 additions & 1 deletion RELEASE_NOTES
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,69 @@ 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 14,282 easyconfig files, for 2,647 different software packages,
The latest version of easybuild-easyconfig provides 14,449 easyconfig files, for 2,667 different software packages,
incl. 36 different (compiler) toolchains.


v4.5.4 (March 31st 2022)
------------------------

update/bugfix release
- added example easyconfig files for 29 new software packages:
- Abseil (#15102), AMS (#13155), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#15052),
Devito (#14984, #15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844),
M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174),
ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035),
porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050),
STRique (#14980), XML-Compile (#15177)
- added additional easyconfigs for various supported software packages, including:
- ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1,
CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0,
ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0,
IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0,
KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a,
MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2,
NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3,
parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1,
RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3,
VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0
- minor enhancements, including:
- add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (#15027)
- add check to verify that patch files touched in PRs have a description in place (#15061)
- add extensions to R v4.1.2 easyconfig: hash (#15098), nabor + harmony (#15117), apluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps (#15141)
- also install rMATS_P commands in rMATS-turbo easyconfig (#15113)
- add extensions to Bioconductor v3.14 easyconfig: chromVAR (#15118), EnsDb.Hsapiens.v79 (#15154), WGCNA (#15178)
- add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (#15176), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (#15190)
- enable running of tests for MEME with gompi/2021b (#15191, #15199)
- various bug fixes, including:
- add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (#14847)
- downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (#14942)
- add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (#14987), optmatch (#14993)
- avoid pollution in the tmp directory when running the AlphaFold tests (#14989)
- consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (#15039)
- fix GBprocesS easyconfig by switching to source tarball created using git_config (#15048)
- add patches for mauveAligner to fix build on RHEL8 (#15049)
- fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (#15051)
- add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (#15054)
- avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (#15055)
- fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 (#15059)
- don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (#15060)
- add M4 as build dependency for CCL-1.12 (#15075)
- configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults (#15086)
- set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (#15097)
- remove disable flag for RTTI in snappy v1.1.9 (#15099)
- fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (#15121)
- clean up PSolver and futile easyconfigs and add dynamic libs (#15148)
- enhance vcflib easyconfigs to also install scripts (#15181)
- add patch to fix shared linking in vcflib (#15203)
- fix failing sanity check for PRINSEQ (#15205)
- other changes:
- use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (#15003)
- disable building of documentation for DBus 1.13.18 (#15010)
- consistently use system toolchain in EasyBuild easyconfigs (#15126)
- use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (#15149)


v4.5.3 (February 11th 2022)
---------------------------

Expand Down
37 changes: 37 additions & 0 deletions easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
name = 'ABAQUS'
version = '2021'
local_hotfix = '2132'
versionsuffix = '-hotfix-%s' % local_hotfix

homepage = 'https://www.simulia.com/products/abaqus_fea.html'
description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit
dynamics FEA."""

toolchain = SYSTEM

sources = [
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar',
'%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar',
# hotfixes
'%%(version)s.FP.CFA.%s.Part_SIMULIA_Documentation.AllOS.tar' % local_hotfix,
'%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix,
'%%(version)s.FP.CFA.%s.Part_SIMULIA_Isight.Linux64.tar' % local_hotfix,
]
checksums = [
'fbc93662c2c0ea9294df79ed9c9678246582d1f63598ad999bbb17fee0dbf54a', # 2021.AM_SIM_Abaqus_Extend.AllOS.1-5.tar
'4433dee911274f559a9372291c007f359108e8e1ab2db6abe570727e1b13741a', # 2021.AM_SIM_Abaqus_Extend.AllOS.2-5.tar
'ddd79bfa40c238b12cc36c2d37ee3a351c21684fd5d6aba402a87051ee27096d', # 2021.AM_SIM_Abaqus_Extend.AllOS.3-5.tar
'c7b5b04388c1a29f4c5ad46da35e2f5e6d2d493832611fc90860644ff837ded0', # 2021.AM_SIM_Abaqus_Extend.AllOS.4-5.tar
'fafb50a0ee12128cd604563eb9b5b845cbeb4383c24df837220cbce847bd5c58', # 2021.AM_SIM_Abaqus_Extend.AllOS.5-5.tar
# 2021.FP.CFA.2132.Part_SIMULIA_Documentation.AllOS.tar
'ac62bdeda3939c83dfc7683eced82816e1dbfdf6e93b7ac5b87967a239438bd4',
# 2021.FP.CFA.2132.Part_SIMULIA_EstPrd.Linux64.tar
'b3e98f05db92c0a15520feef3494fb80d260d3ecdb67610059c3fd229426d78b',
# 2021.FP.CFA.2132.Part_SIMULIA_Isight.Linux64.tar
'b27a90484f89989c3f27133239a85483ee24092af5d8a2159681b2cc1fada46c',
]

moduleclass = 'cae'
38 changes: 38 additions & 0 deletions easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
easyblock = 'Tarball'

name = 'AMS'
version = '2020.102'
versionsuffix = '-intelmpi'

homepage = 'https://www.scm.com/amsterdam-modeling-suite/'
description = """
The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials
science, from quantum mechanics to fluid thermodynamics.
"""

toolchain = {'name': 'iimpi', 'version': '2020b'}

sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz']
checksums = ['8a68eef268d7eb53ea1e10f66a48a8280f4dadae585999096ba1c246e88989db']

dependencies = [('libGLU', '9.0.1')]

keepsymlinks = True

sanity_check_paths = {
'files': [],
'dirs': ['atomicdata', 'bin', 'examples'],
}

modextrapaths = {
'AMSHOME': '',
'AMSBIN': 'bin',
'AMSRESOURCES': 'atomicdata',
}

modloadmsg = """These environment variables need to be defined before using AMS:
* $SCMLICENSE: path to AMS license file
* $SCM_TMPDIR: path to user scratch directory
"""

moduleclass = 'chem'
64 changes: 64 additions & 0 deletions easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
# Updated by: Pavel Grochal (INUITS)
# License: GPLv2

easyblock = 'ConfigureMake'

name = 'AUGUSTUS'
version = '3.4.0'

homepage = 'https://bioinf.uni-greifswald.de/augustus/'
description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"

toolchain = {'name': 'foss', 'version': '2021b'}

# https://github.com/Gaius-Augustus/Augustus/archive
github_account = 'Gaius-Augustus'
source_urls = [GITHUB_SOURCE]
sources = ['v%(version)s.tar.gz']
patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch']
checksums = [
'2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz
'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # AUGUSTUS-3.4.0_fix-hardcoding.patch
]

builddependencies = [
('Python', '3.9.6'),
]

dependencies = [
('zlib', '1.2.11'),
('Boost', '1.77.0'),
('GSL', '2.7'),
('SAMtools', '1.14'),
('HTSlib', '1.14'), # also provides tabix
('BCFtools', '1.14'),
('lpsolve', '5.5.2.11'),
('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
('BamTools', '2.5.2'),
('SQLite', '3.36'),
]

skipsteps = ['configure']

# run "make clean" to avoid using binaries included with the source tarball
prebuildopts = "make clean && "

buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" LINK.cc="$CXX" '
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'
31 changes: 31 additions & 0 deletions easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
easyblock = 'CMakeMake'

name = 'Abseil'
version = '20210324.2'

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': '11.2.0'}
toolchainopts = {'pic': True, 'cstd': 'c++11'}

source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags']
sources = ['%(version)s.tar.gz']
checksums = ['59b862f50e710277f8ede96f083a5bb8d7c9595376146838b9580be90374ee1f']

builddependencies = [
('binutils', '2.37'),
('CMake', '3.21.1'),
]

configopts = '-DBUILD_SHARED_LIBS=ON '

sanity_check_paths = {
'files': ['lib/libabsl_base.%s' % SHLIB_EXT],
'dirs': ['include/absl'],
}

moduleclass = 'lib'
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,8 @@ components = [
'AlphaFold-2.0.0_n-cpu.patch',
'AlphaFold-2.1.0_fix-scp-path.patch',
'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
'AlphaFold-2.0.1_relax_gpu.patch'
'AlphaFold-2.0.1_relax_gpu.patch',
'AlphaFold-2.1_fix-alphafold-tests.patch',
],
'checksums': [
'1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz
Expand All @@ -89,6 +90,8 @@ components = [
'5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch
'1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch
'3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch
# AlphaFold-2.1_fix-alphafold-tests.patch
'1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588',
],
'start_dir': 'alphafold-%(version)s',
'use_pip': True,
Expand Down
Loading

0 comments on commit 478fa1d

Please sign in to comment.