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Merge pull request #14829 from easybuilders/4.5.x
release EasyBuild v4.5.2
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| Original file line number | Diff line number | Diff line change |
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| ## | ||
| # Author: Robert Mijakovic <robert.mijakovic@lxp.lu> | ||
| ## | ||
| easyblock = 'Binary' | ||
|
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| name = 'AMD-uProf' | ||
| version = '3.4.502' | ||
|
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| homepage = 'https://developer.amd.com/amd-uprof/' | ||
| description = """AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD | ||
| operating systems. It allows developers to better understand the runtime performance of their application and | ||
| to identify ways to improve its performance.""" | ||
|
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| toolchain = SYSTEM | ||
|
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| source_urls = ['https://developer.amd.com/wordpress/media/files/'] | ||
| sources = ['AMDuProf_Linux_x64_%(version)s.tar.bz2'] | ||
| checksums = ['891463c0e4f20e1c67a145441e983c863156a52716234cd8d5a96a8d09635ba7'] | ||
|
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| extract_sources = True | ||
|
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| sanity_check_paths = { | ||
| 'files': ['include/AMDTPowerProfileApi.h', 'lib/x64/libAMDProfileController.a', | ||
| 'bin/libAMDThreadProfileAPI.%s' % SHLIB_EXT, 'bin/AMDuProf'], | ||
| 'dirs': ['Examples'] | ||
| } | ||
|
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| sanity_check_commands = ['AMDuProfCLI info --system'] | ||
|
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| modextrapaths = { | ||
| 'LD_LIBRARY_PATH': 'bin' | ||
| } | ||
|
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| moduleclass = 'perf' |
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| ## | ||
| # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild | ||
| # | ||
| # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA | ||
| # Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch> | ||
| # License:: MIT/GPL | ||
| # $Id$ | ||
| # | ||
| # This work implements a part of the HPCBIOS project and is a component of the policy: | ||
| # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html | ||
| ## | ||
|
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| easyblock = 'ConfigureMake' | ||
|
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| name = 'AMOS' | ||
| version = '3.1.0' | ||
|
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| homepage = 'http://amos.sourceforge.net' | ||
| description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2021b'} | ||
| toolchainopts = {'pic': True, 'cstd': 'c++98'} | ||
|
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| source_urls = [SOURCEFORGE_SOURCE] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| patches = ['AMOS-%(version)s_GCC-4.7.patch'] | ||
| checksums = [ | ||
| '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz | ||
| '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch | ||
| ] | ||
|
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| dependencies = [ | ||
| ('expat', '2.4.1'), | ||
| ('MUMmer', '4.0.0beta2'), | ||
| ] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], | ||
| 'dirs': [] | ||
| } | ||
|
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| parallel = 1 # make crashes otherwise | ||
|
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| moduleclass = 'bio' |
53 changes: 53 additions & 0 deletions
53
easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb
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|---|---|---|
| @@ -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 <rob.qiao@flinders.edu.au> | ||
| # License:: Custom | ||
| # | ||
| # Notes:: | ||
| ## | ||
|
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| easyblock = 'PythonPackage' | ||
|
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| name = 'ANGEL' | ||
| version = '3.0' | ||
| versionsuffix = '-Python-%(pyver)s' | ||
|
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| homepage = 'https://github.com/PacificBiosciences/ANGEL' | ||
| description = """ANGEL: Robust Open Reading Frame prediction""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2019a'} | ||
| toolchainopts = {'usempi': True} | ||
|
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| source_urls = ['https://github.com/PacificBiosciences/ANGEL/archive'] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| checksums = ['a0319553055d3dfc84a4f732ed246c180c23ee9c397810c96acd7940721ae57d'] | ||
|
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| dependencies = [ | ||
| ('Python', '3.7.2'), | ||
| ('Biopython', '1.73'), | ||
| ('scikit-learn', '0.20.3'), | ||
| ] | ||
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| download_dep_fail = True | ||
| use_pip = True | ||
|
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| local_bin_files = [ | ||
| 'dumb_predict.py', | ||
| 'angel_make_training_set.py', | ||
| 'angel_train.py', | ||
| 'angel_predict.py', | ||
| 'angel_compare_files.py' | ||
| ] | ||
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| options = {'modulename': False} | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in local_bin_files], | ||
| 'dirs': [], | ||
| } | ||
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| sanity_pip_check = True | ||
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| moduleclass = 'bio' |
37 changes: 37 additions & 0 deletions
37
easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb
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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 = 'AdapterRemoval' | ||
| version = '2.3.2' | ||
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| homepage = 'https://github.com/MikkelSchubert/adapterremoval' | ||
| description = """AdapterRemoval searches for and removes remnant adapter sequences | ||
| from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases | ||
| from the 3' end of reads following adapter removal.""" | ||
|
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| toolchain = {'name': 'GCC', 'version': '11.2.0'} | ||
| toolchainopts = {'pic': True} | ||
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| github_account = 'MikkelSchubert' | ||
| source_urls = [GITHUB_LOWER_SOURCE] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] | ||
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| dependencies = [ | ||
| ('bzip2', '1.0.8'), | ||
| ('zlib', '1.2.11'), | ||
| ] | ||
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| skipsteps = ['configure'] | ||
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| installopts = "PREFIX=%(installdir)s" | ||
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| runtest = 'test' | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/%(name)s'], | ||
| 'dirs': ['share'] | ||
| } | ||
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| sanity_check_commands = [('%(name)s', '--version')] | ||
|
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| # author: Jillian Rowe <jillian.e.rowe@gmail.com> | ||
| # config upgrade to v5.1.0 by Adam Huffman <adam.huffman@bdi.ox.ac.uk> | ||
| # config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, | ||
| # 2020.2, 2020.11, 2021.11 by J. Hein <joachim.hein@lunarc.lu.se> | ||
| # config upgrade to 2019.03 by Davide Vanzo <davide.vanzo@vanderbilt.edu> | ||
| easyblock = 'EB_Anaconda' | ||
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| name = 'Anaconda3' | ||
| version = '2021.11' | ||
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| homepage = 'https://www.anaconda.com' | ||
| description = """Built to complement the rich, open source Python community, | ||
| the Anaconda platform provides an enterprise-ready data analytics platform | ||
| that empowers companies to adopt a modern open data science analytics architecture. | ||
| """ | ||
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| toolchain = SYSTEM | ||
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| source_urls = ['https://repo.anaconda.com/archive/'] | ||
| sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] | ||
|
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| checksums = [ | ||
| { | ||
| '%(name)s-%(version)s-Linux-x86_64.sh': 'fedf9e340039557f7b5e8a8a86affa9d299f5e9820144bd7b92ae9f7ee08ac60', | ||
| '%(name)s-%(version)s-Linux-ppc64le.sh': '7eb6a95925ee756240818599f8dcbba7a155adfb05ef6cd5336aa3c083de65f3', | ||
| } | ||
| ] | ||
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| moduleclass = 'lang' |
22 changes: 22 additions & 0 deletions
22
easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb
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| name = 'Armadillo' | ||
| version = "10.7.5" | ||
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| homepage = 'http://arma.sourceforge.net/' | ||
| description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards | ||
| a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, | ||
| as well as a subset of trigonometric and statistics functions.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2021a'} | ||
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| source_urls = ['https://sourceforge.net/projects/arma/files'] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| checksums = ['5d0d9fd6b34efcba6a6fceff54c0d2d13fcbe915d7af8a30c5e72cf317d2094f'] | ||
|
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| dependencies = [ | ||
| ('Boost', '1.76.0'), | ||
| ('arpack-ng', '3.8.0'), | ||
| ] | ||
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| builddependencies = [('CMake', '3.20.1')] | ||
|
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| moduleclass = 'numlib' |
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| Original file line number | Diff line number | Diff line change |
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| easyblock = 'CMakeMake' | ||
|
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| name = 'Arrow' | ||
| version = '0.17.1' | ||
|
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| homepage = 'https://arrow.apache.org' | ||
| description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform | ||
| for in-memory data.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2020b'} | ||
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| source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] | ||
| sources = ['apache-arrow-%(version)s.tar.gz'] | ||
| patches = ['Arrow-0.17.1_fix-arm.patch'] | ||
| checksums = [ | ||
| 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz | ||
| 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch | ||
| ] | ||
|
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| builddependencies = [ | ||
| ('CMake', '3.18.4'), | ||
| ('Autotools', '20200321'), | ||
| ('flex', '2.6.4'), | ||
| ('Bison', '3.7.1'), | ||
| ('pkg-config', '0.29.2'), | ||
| ] | ||
|
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| # Arrow strongly prefers included jemalloc, so not including it as a dependency | ||
| dependencies = [ | ||
| ('Python', '3.8.6'), | ||
| ('SciPy-bundle', '2020.11',), # for numpy | ||
| ('Boost', '1.74.0'), | ||
| ] | ||
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| start_dir = 'cpp' | ||
|
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| # see https://arrow.apache.org/docs/python/development.html | ||
| configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " | ||
| configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" | ||
|
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| # also install Python bindings | ||
| local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " | ||
| local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " | ||
| local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " | ||
| local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " | ||
| local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " | ||
| local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." | ||
| postinstallcmds = [local_install_pyarrow_cmds] | ||
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| modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} | ||
|
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| sanity_check_paths = { | ||
| 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, | ||
| 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], | ||
| 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
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| sanity_check_commands = [ | ||
| "python -c 'import pyarrow'", | ||
| "python -c 'import pyarrow.parquet'", | ||
| ] | ||
|
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| moduleclass = 'data' |
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