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41 changes: 41 additions & 0 deletions
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easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023a.eb
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| # 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': '2023a'} | ||
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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', '5.36.1'), | ||
| ('any2fasta', '0.4.2'), | ||
| ('BioPerl', '1.7.8'), | ||
| ('BLAST+', '2.14.1'), | ||
| ] | ||
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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 $EBROOTABRICATE/db\n" | ||
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| moduleclass = 'bio' |
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| easyblock = 'CMakeMake' | ||
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| name = 'ALL' | ||
| version = '0.9.2' | ||
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| homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing' | ||
| description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic | ||
| domain-based load balancing into particle based simulation codes. The library | ||
| is developed in the Simulation Laboratory Molecular Systems of the Jülich | ||
| Supercomputing Centre at Forschungszentrum Jülich.""" | ||
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| toolchain = {'name': 'foss', 'version': '2023b'} | ||
| toolchainopts = {'usempi': True} | ||
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| source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"] | ||
| sources = ['loadbalancing-v%(version)s.tar.gz'] | ||
| checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] | ||
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| builddependencies = [ | ||
| ('CMake', '3.27.6'), | ||
| ('Boost', '1.83.0'), # only needed for tests | ||
| ] | ||
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| dependencies = [ | ||
| ('VTK', '9.3.0'), | ||
| ] | ||
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| configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' | ||
| configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' | ||
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| runtest = 'test' | ||
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| 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'], | ||
| } | ||
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| moduleclass = 'lib' |
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easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.12.8-gompi-2023a.eb
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| easyblock = 'MakeCp' | ||
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| name = 'AMRFinderPlus' | ||
| version = '3.12.8' | ||
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| homepage = 'https://github.com/ncbi/amr' | ||
| description = """This software and the accompanying database are designed to find acquired antimicrobial | ||
| resistance genes and some point mutations in protein or assembled nucleotide sequences.""" | ||
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| toolchain = {'name': 'gompi', 'version': '2023a'} | ||
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| github_account = 'ncbi' | ||
| source_urls = ['https://github.com/ncbi/amr/archive/'] | ||
| sources = ['amrfinder_v%(version)s.tar.gz'] | ||
| checksums = ['a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0'] | ||
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| dependencies = [ | ||
| ('BLAST+', '2.14.1'), | ||
| ('HMMER', '3.4'), | ||
| ('cURL', '8.0.1') | ||
| ] | ||
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| # Binaries are installed to the root of the installation, so add that root to the PATH: | ||
| modextrapaths = {'PATH': ''} | ||
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| # a list of binary files that will be produced | ||
| local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check', | ||
| 'fasta_extract', 'gff_check'] | ||
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| files_to_copy = local_binaries | ||
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| sanity_check_paths = { | ||
| 'files': local_binaries, | ||
| 'dirs': [], | ||
| } | ||
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| sanity_check_commands = [ | ||
| ('amrfinder', '-h') | ||
| ] | ||
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| moduleclass = 'bio' |
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| name = 'AOCC' | ||
| version = '4.2.0' | ||
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| homepage = 'https://developer.amd.com/amd-aocc/' | ||
| description = """AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages. | ||
| It supports target-dependent and target-independent optimizations. It is highly optimized for x86 targets, | ||
| especially for AMD “Zen”-based processors giving a performance edge for time critical HPC and other | ||
| applications over other compilers.""" | ||
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| # Clang also depends on libstdc++ during runtime, but this dependency is | ||
| # already specified as the toolchain. | ||
| toolchain = {'name': 'GCCcore', 'version': '13.3.0'} | ||
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| source_urls = [ | ||
| 'https://download.amd.com/developer/eula/%(namelower)s/%(namelower)s-%(version_major)s-%(version_minor)s' | ||
| ] | ||
| sources = ['%(namelower)s-compiler-%(version)s.tar'] | ||
| checksums = ['ed5a560ec745b24dc0685ccdcbde914843fb2f2dfbfce1ba592de4ffbce1ccab'] | ||
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| dependencies = [ | ||
| ('binutils', '2.42'), | ||
| ('ncurses', '6.5'), | ||
| ('zlib', '1.3.1'), | ||
| ('libxml2', '2.12.7'), | ||
| ] | ||
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| clangversion = '16.0.3' | ||
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| moduleclass = 'compiler' |
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