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Merge pull request #18279 from easybuilders/4.8.x
release EasyBuild v4.8.0
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35 changes: 35 additions & 0 deletions
35
easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb
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| Original file line number | Diff line number | Diff line change |
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| easyblock = 'Tarball' | ||
|
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| name = '3d-dna' | ||
| version = '180922' | ||
| versionsuffix = '-Python-%(pyver)s' | ||
| local_githash = '529ccf46599825b3047e58a69091d599e9858a19' | ||
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| homepage = 'https://github.com/theaidenlab/3d-dna' | ||
| description = """3D de novo assembly (3D DNA) pipeline""" | ||
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| toolchain = {'name': 'GCCcore', 'version': '8.2.0'} | ||
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| source_urls = ['https://github.com/theaidenlab/%(name)s/archive'] | ||
| sources = [{'download_filename': '%s.zip' % local_githash, 'filename': SOURCE_ZIP}] | ||
| checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] | ||
|
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| dependencies = [ | ||
| ('Python', '2.7.15'), | ||
| ('LASTZ', '1.02.00'), | ||
| ('Java', '1.8', '', SYSTEM), | ||
| ('parallel', '20190622'), | ||
| ] | ||
|
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| postinstallcmds = ['chmod 755 %(installdir)s/*.sh'] | ||
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| sanity_check_paths = { | ||
| 'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'], | ||
| 'dirs': [], | ||
| } | ||
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| sanity_check_commands = ["run-asm-pipeline.sh --help"] | ||
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| modextrapaths = {'PATH': ''} | ||
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| # | ||
| easyblock = 'ConfigureMake' | ||
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| name = 'ABINIT' | ||
| version = '9.2.1' | ||
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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': '2019b'} | ||
| toolchainopts = {'usempi': True, 'pic': True} | ||
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] | ||
|
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| builddependencies = [ | ||
| ('Python', '3.7.4'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '4.3.4'), | ||
| ('netCDF', '4.7.1'), | ||
| ('netCDF-Fortran', '4.5.2'), | ||
| ('HDF5', '1.10.5'), | ||
| ] | ||
|
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| # Ensure MPI. | ||
| configopts = '--with-mpi="yes" --enable-openmp="no" ' | ||
|
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| # BLAS/Lapack | ||
| configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="-L${EBROOTOPENBLAS}/lib -lopenblas" ' | ||
|
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| # FFTW3 support | ||
| configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${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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| # make sure --free-line-length-none is added to FCFLAGS | ||
| configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' | ||
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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' |
57 changes: 57 additions & 0 deletions
57
easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| # | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'ABINIT' | ||
| version = '9.2.1' | ||
|
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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': '2019b'} | ||
| toolchainopts = {'usempi': True, 'pic': True} | ||
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| source_urls = ['https://www.abinit.org/sites/default/files/packages/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] | ||
|
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| builddependencies = [ | ||
| ('Python', '3.7.4'), | ||
| ] | ||
| dependencies = [ | ||
| ('libxc', '4.3.4'), | ||
| ('netCDF', '4.7.1'), | ||
| ('netCDF-Fortran', '4.5.2'), | ||
| ('HDF5', '1.10.5'), | ||
| ] | ||
|
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| # Ensure MPI with intel wrappers. | ||
| configopts = '--with-mpi="yes" --enable-openmp="no" ' | ||
| configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' | ||
|
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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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| # `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' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| # easybuild easyconfig | ||
| # | ||
| # John Dey <jfdey@fredhutch.org> Fred Hutchinson Cancer Center | ||
| # Thomas Eylenbosch - Gluo NV | ||
| # | ||
| easyblock = 'Bundle' | ||
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| name = 'AGAT' | ||
| version = '1.1.0' | ||
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| 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.""" | ||
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| toolchain = {'name': 'GCC', 'version': '12.2.0'} | ||
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| builddependencies = [('binutils', '2.39')] | ||
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| dependencies = [ | ||
| ('Perl', '5.36.0'), | ||
| ('BioPerl', '1.7.8'), | ||
| ] | ||
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| exts_defaultclass = 'PerlModule' | ||
| exts_filter = ("perl -e 'require %(ext_name)s'", '') | ||
|
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| 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': ['38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002'], | ||
| }), | ||
| ] | ||
|
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| modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} | ||
|
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| sanity_check_paths = { | ||
| 'files': [], | ||
| 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], | ||
| } | ||
|
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| sanity_check_commands = ['agat_convert_bed2gff.pl --help'] | ||
| moduleclass = 'bio' |
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