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Merge pull request #10650 from easybuilders/4.2.x
release EasyBuild 4.2.1
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30 changes: 30 additions & 0 deletions
30
easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.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 = '4ti2' | ||
| version = '1.6.9' | ||
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| homepage = 'https://4ti2.github.io/' | ||
| description = """A software package for algebraic, geometric and combinatorial problems on linear spaces""" | ||
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| toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} | ||
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| github_account = '4ti2' | ||
| source_urls = [GITHUB_SOURCE] | ||
| sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))] | ||
| checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4'] | ||
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| dependencies = [ | ||
| ('GMP', '6.1.2'), | ||
| ('GLPK', '4.65'), | ||
| ] | ||
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| builddependencies = [('Autotools', '20180311')] | ||
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| preconfigopts = './autogen.sh && ' | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']], | ||
| 'dirs': ['include/4ti2', 'lib', 'share/4ti2'] | ||
| } | ||
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| moduleclass = 'math' |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,34 @@ | ||
| easyblock = 'Tarball' | ||
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| name = 'ADF' | ||
| version = '2019.303' | ||
| versionsuffix = '-intelmpi' | ||
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| homepage = 'https://www.scm.com/ADF/' | ||
| description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and | ||
| predict chemical structure and reactivity with density functional theory (DFT).""" | ||
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| toolchain = SYSTEM | ||
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| sources = ['adf%(version)s.pc64_linux.intelmpi.bin.tgz'] | ||
| checksums = ['62f73d2bc37bfc7891c1b10e83abccae317f7751f2a7b88976b24d16ef2b771a'] | ||
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| keepsymlinks = True | ||
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| sanity_check_paths = { | ||
| 'files': [], | ||
| 'dirs': ['atomicdata', 'bin', 'examples'], | ||
| } | ||
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| modextravars = { | ||
| 'ADFHOME': '%(installdir)s', | ||
| 'ADFBIN': '%(installdir)s/bin', | ||
| 'ADFRESOURCES': '%(installdir)s/atomicdata', | ||
| } | ||
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| modloadmsg = """These environment variables need to be defined before using ADF: | ||
| * $SCMLICENSE: path to ADF license file | ||
| * $SCM_TMPDIR: path to user scratch directory | ||
| """ | ||
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| moduleclass = 'chem' |
35 changes: 35 additions & 0 deletions
35
easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-iccifort-2019.5.281.eb
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,35 @@ | ||
| # This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ | ||
| # Author: Pablo Escobar Lopez | ||
| # sciCORE - University of Basel | ||
| # SIB Swiss Institute of Bioinformatics | ||
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| easyblock = 'CmdCp' | ||
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| name = 'ARAGORN' | ||
| version = '1.2.38' | ||
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| # HTTPS not working | ||
| homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/' | ||
| description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences" | ||
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| toolchain = {'name': 'iccifort', 'version': '2019.5.281'} | ||
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| source_urls = ['http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/'] | ||
| sources = ['%(namelower)s%(version)s.tgz'] | ||
| checksums = ['4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126'] | ||
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| cmds_map = [(".*", "$CC $CFLAGS -o aragorn aragorn%(version)s.c")] | ||
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| files_to_copy = [ | ||
| (['aragorn'], 'bin'), | ||
| (['aragorn.1'], 'share/man/man1'), | ||
| ] | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/aragorn'], | ||
| 'dirs': ['share/man'], | ||
| } | ||
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| sanity_check_commands = ['aragorn --help'] | ||
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,39 @@ | ||
| easyblock = 'MesonNinja' | ||
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| name = 'ATK' | ||
| version = '2.36.0' | ||
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| homepage = 'https://developer.gnome.org/atk/' | ||
| description = """ | ||
| ATK provides the set of accessibility interfaces that are implemented by other | ||
| toolkits and applications. Using the ATK interfaces, accessibility tools have | ||
| full access to view and control running applications. | ||
| """ | ||
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| toolchain = {'name': 'GCCcore', 'version': '9.3.0'} | ||
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| source_urls = [FTPGNOME_SOURCE] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] | ||
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| builddependencies = [ | ||
| ('binutils', '2.34'), | ||
| ('Meson', '0.53.2', '-Python-3.8.2'), | ||
| ('Ninja', '1.10.0'), | ||
| ('pkg-config', '0.29.2'), | ||
| ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), | ||
| ] | ||
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| dependencies = [ | ||
| ('GLib', '2.64.1'), | ||
| ] | ||
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| configopts = "--buildtype=release --default-library=both " | ||
| configopts += "-Dintrospection=true " | ||
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| sanity_check_paths = { | ||
| 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], | ||
| 'dirs': [], | ||
| } | ||
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| moduleclass = 'vis' |
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63 changes: 63 additions & 0 deletions
63
easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,63 @@ | ||
| # Updated by: Pavel Grochal (INUITS) | ||
| # License: GPLv2 | ||
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| easyblock = 'ConfigureMake' | ||
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| name = 'AUGUSTUS' | ||
| version = '3.3.3' | ||
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| # HTTPS doesn't work | ||
| homepage = 'http://bioinf.uni-greifswald.de/augustus/' | ||
| description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" | ||
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| toolchain = {'name': 'intel', 'version': '2019b'} | ||
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| # https://github.com/Gaius-Augustus/Augustus/archive | ||
| github_account = 'Gaius-Augustus' | ||
| source_urls = [GITHUB_SOURCE] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| patches = [ | ||
| '%(name)s-%(version)s_fix-hardcoding.patch', | ||
| ] | ||
| checksums = [ | ||
| '2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4', # v3.3.3.tar.gz | ||
| '414907ab65cd27df33508f7d0c2fde4cc5e6ffd9fb7be9357d1488851e480e94', # AUGUSTUS-3.3.3_fix-hardcoding.patch | ||
| ] | ||
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| dependencies = [ | ||
| ('zlib', '1.2.11'), | ||
| ('Boost', '1.71.0'), | ||
| ('GSL', '2.6'), | ||
| ('SAMtools', '1.10'), | ||
| ('HTSlib', '1.10.2'), # also provides tabix | ||
| ('BCFtools', '1.10.2'), | ||
| ('lpsolve', '5.5.2.5'), | ||
| ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), | ||
| ('BamTools', '2.5.1'), | ||
| ('SQLite', '3.29.0'), | ||
| ] | ||
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| skipsteps = ['configure'] | ||
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| # run "make clean" to avoid using binaries included with the source tarball | ||
| prebuildopts = "make clean && " | ||
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| buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" ' | ||
| installopts = 'INSTALLDIR=%(installdir)s ' | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', | ||
| 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', | ||
| 'bin/load2sqlitedb', 'bin/prepareAlign'], | ||
| 'dirs': ['config', 'scripts'], | ||
| } | ||
| sanity_check_commands = ['augustus --help'] | ||
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| modextrapaths = {'PATH': 'scripts'} | ||
| modextravars = { | ||
| 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', | ||
| 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', | ||
| 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', | ||
| } | ||
|
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| moduleclass = 'bio' |
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