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Merge pull request #14542 from easybuilders/4.5.x
release EasyBuild v4.5.1
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| Original file line number | Diff line number | Diff line change |
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| easyblock = 'ConfigureMake' | ||
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| name = 'ABINIT' | ||
| version = '9.4.2' | ||
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| homepage = 'https://www.abinit.org/' | ||
| description = """ABINIT is a package whose main program allows one to find the total energy, | ||
| charge density and electronic structure of systems made of electrons and nuclei (molecules | ||
| and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a | ||
| planewave or wavelet basis.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2021a'} | ||
| toolchainopts = {'usempi': True, 'pic': True} | ||
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc'] | ||
|
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| builddependencies = [ | ||
| ('Python', '3.9.5'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '5.1.5'), | ||
| ('netCDF', '4.8.0'), | ||
| ('netCDF-Fortran', '4.5.3'), | ||
| ('HDF5', '1.10.7'), | ||
| ('Wannier90', '3.1.0'), | ||
| ] | ||
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| # Needed due to changes in GCC10. | ||
| configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' | ||
| configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' | ||
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| # Ensure MPI | ||
| configopts += '--with-mpi="yes" --enable-openmp="no" ' | ||
| # configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' | ||
|
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| # BLAS/Lapack from OpenBLAS | ||
| configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' | ||
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| # FFTW | ||
| configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' | ||
|
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| # libxc support | ||
| configopts += '--with-libxc=${EBROOTLIBXC} ' | ||
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| # hdf5/netcdf4 support | ||
| configopts += '--with-netcdf="${EBROOTNETCDF}" ' | ||
| configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' | ||
| configopts += '--with-hdf5="${EBROOTHDF5}" ' | ||
|
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| # Wannier90 | ||
| configopts += '--with-wannier90="${EBROOTWANNIER90}" ' | ||
| preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' | ||
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| # 'make check' is just executing some basic unit tests. | ||
| # Also running 'make tests_v1' to have some basic validation | ||
| runtest = "check && make test_v1" | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], | ||
| 'dirs': ['lib/pkgconfig'], | ||
| } | ||
|
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| moduleclass = 'chem' |
68 changes: 68 additions & 0 deletions
68
easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'ABINIT' | ||
| version = '9.6.2' | ||
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| homepage = 'https://www.abinit.org/' | ||
| description = """ | ||
| ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of | ||
| systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using | ||
| pseudopotentials and a planewave or wavelet basis. | ||
| """ | ||
|
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| toolchain = {'name': 'intel', 'version': '2021a'} | ||
| toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} | ||
|
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] | ||
|
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| builddependencies = [ | ||
| ('Python', '3.9.5'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '5.1.5'), | ||
| ('netCDF', '4.8.0'), | ||
| ('netCDF-Fortran', '4.5.3'), | ||
| ('HDF5', '1.10.7'), | ||
| ('Wannier90', '3.1.0'), | ||
| ] | ||
|
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| # Ensure MPI with intel wrappers. | ||
| configopts = '--with-mpi="yes" ' | ||
| configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' | ||
|
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| # Enable OpenMP | ||
| configopts += '--enable-openmp="yes" ' | ||
|
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| # BLAS/Lapack from MKL | ||
| configopts += '--with-linalg-flavor=mkl ' | ||
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| # FFTW from MKL | ||
| configopts += '--with-fft-flavor=dfti ' | ||
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| # libxc support | ||
| configopts += '--with-libxc=${EBROOTLIBXC} ' | ||
|
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| # hdf5/netcdf4 support | ||
| configopts += '--with-netcdf="${EBROOTNETCDF}" ' | ||
| configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' | ||
| configopts += '--with-hdf5="${EBROOTHDF5}" ' | ||
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| # Wannier90 | ||
| configopts += '--with-wannier90="${EBROOTWANNIER90}" ' | ||
| preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' | ||
|
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| # Enable double precision for GW calculations | ||
| configopts += '--enable-gw-dpc ' | ||
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| # 'make check' is just executing some basic unit tests. | ||
| # Also running 'make tests_v1' to have some basic validation | ||
| runtest = "check && make test_v1" | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], | ||
| 'dirs': ['lib/pkgconfig'], | ||
| } | ||
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| moduleclass = 'chem' |
71 changes: 71 additions & 0 deletions
71
easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'ABINIT' | ||
| version = '9.6.2' | ||
|
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| homepage = 'https://www.abinit.org/' | ||
| description = """ | ||
| ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of | ||
| systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using | ||
| pseudopotentials and a planewave or wavelet basis. | ||
| """ | ||
|
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| toolchain = {'name': 'intel', 'version': '2021b'} | ||
| toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} | ||
|
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] | ||
|
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| builddependencies = [ | ||
| ('Python', '3.9.6'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '5.1.6'), | ||
| ('netCDF', '4.8.1'), | ||
| ('netCDF-Fortran', '4.5.3'), | ||
| ('HDF5', '1.12.1'), | ||
| ('Wannier90', '3.1.0'), | ||
| ] | ||
|
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| # Ensure MPI with intel wrappers. | ||
| configopts = '--with-mpi="yes" ' | ||
| configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' | ||
|
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| # Enable OpenMP | ||
| configopts += '--enable-openmp="yes" ' | ||
|
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| # BLAS/Lapack from MKL | ||
| configopts += '--with-linalg-flavor=mkl ' | ||
|
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| # FFTW from MKL | ||
| configopts += '--with-fft-flavor=dfti ' | ||
|
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| # libxc support | ||
| configopts += '--with-libxc=${EBROOTLIBXC} ' | ||
|
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| # hdf5/netcdf4 support | ||
| configopts += '--with-netcdf="${EBROOTNETCDF}" ' | ||
| configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' | ||
| configopts += '--with-hdf5="${EBROOTHDF5}" ' | ||
|
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| # Wannier90 | ||
| configopts += '--with-wannier90="${EBROOTWANNIER90}" ' | ||
| preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' | ||
|
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| # Enable double precision for GW calculations | ||
| configopts += '--enable-gw-dpc ' | ||
|
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| # Enable OpenMP | ||
| configopts += '--enable-openmp ' | ||
|
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| # 'make check' is just executing some basic unit tests. | ||
| # Also running 'make tests_v1' to have some basic validation | ||
| runtest = "check && make test_v1" | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], | ||
| 'dirs': ['lib/pkgconfig'], | ||
| } | ||
|
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| moduleclass = 'chem' |
41 changes: 41 additions & 0 deletions
41
easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| # Author: Pavel Grochal (INUITS) | ||
| # License: GPLv2 | ||
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| easyblock = 'Tarball' | ||
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| name = 'ABRicate' | ||
| version = '1.0.0' | ||
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| homepage = 'https://github.com/tseemann/abricate' | ||
| description = "Mass screening of contigs for antimicrobial and virulence genes" | ||
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| toolchain = {'name': 'gompi', 'version': '2021a'} | ||
|
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| # https://github.com/tseemann/abricate | ||
| github_account = 'tseemann' | ||
| source_urls = [GITHUB_LOWER_SOURCE] | ||
| sources = ['v%(version)s.zip'] | ||
| checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] | ||
|
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| dependencies = [ | ||
| ('Perl', '5.32.1'), | ||
| ('any2fasta', '0.4.2'), | ||
| ('BioPerl', '1.7.8'), | ||
| ('BLAST+', '2.11.0'), | ||
| ] | ||
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| postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/abricate', 'bin/abricate-get_db'], | ||
| 'dirs': ['db'], | ||
| } | ||
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| sanity_check_commands = [ | ||
| "abricate --help", | ||
| "abricate --list", | ||
| ] | ||
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| modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" | ||
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| moduleclass = 'bio' |
46 changes: 46 additions & 0 deletions
46
easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| easyblock = 'MakeCp' | ||
|
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| name = 'ANIcalculator' | ||
| version = '1.0' | ||
|
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| homepage = 'https://ani.jgi.doe.gov/html/home.php' | ||
| description = """This tool will calculate the bidirectional average nucleotide identity (gANI) and | ||
| Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file | ||
| (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes | ||
| can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence | ||
| of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.""" | ||
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| toolchain = {'name': 'GCCcore', 'version': '10.3.0'} | ||
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| source_urls = ['https://ani.jgi.doe.gov/download_files/'] | ||
| sources = ['%(name)s_v%(version_major)s.tgz'] | ||
| checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] | ||
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| dependencies = [ | ||
| ('Perl', '5.32.1'), | ||
| ('libnsl', '1.3.0'), | ||
| ] | ||
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| skipsteps = ['build'] | ||
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| # The source tarball also includes Log4perl 1.44. | ||
| # Instead of copying this, we use the version from the Perl module. | ||
| files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] | ||
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| # Fix permissions on binaries and README.txt, | ||
| postinstallcmds = [ | ||
| 'chmod a+x %(installdir)s/bin/*', | ||
| 'chmod -x %(installdir)s/README.txt', | ||
| ] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], | ||
| 'dirs': [], | ||
| } | ||
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| sanity_check_commands = [ | ||
| 'ANIcalculator -help', | ||
| 'nsimscan -h', | ||
| ] | ||
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| moduleclass = 'bio' |
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