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29 changes: 29 additions & 0 deletions
29
easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-Port-better-to-NVHPC.patch
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From 632282145ba1d617f480cde74eef938826fef4d5 Mon Sep 17 00:00:00 2001 | ||
From: Paul Eggert <[email protected]> | ||
Date: Thu, 16 Jan 2025 11:24:12 -0800 | ||
Subject: Port better to NVHPC | ||
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||
See <https://savannah.gnu.org/support/?111172>. | ||
* lib/autoconf/fortran.m4 (_AC_FC_LIBRARY_LDFLAGS): | ||
Ignore -l options with embedded '='. | ||
--- | ||
lib/autoconf/fortran.m4 | 2 +- | ||
1 file changed, 1 insertion(+), 1 deletion(-) | ||
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diff --git a/lib/autoconf/fortran.m4 b/lib/autoconf/fortran.m4 | ||
index 0fc7545d..4c39607c 100644 | ||
--- a/lib/autoconf/fortran.m4 | ||
+++ b/lib/autoconf/fortran.m4 | ||
@@ -664,7 +664,7 @@ while test $[@%:@] != 1; do | ||
;; | ||
# Ignore these flags. | ||
-lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -little \ | ||
- |-LANG:=* | -LIST:* | -LNO:* | -link) | ||
+ | -[[lLR]]*=* | -LIST:* | -LNO:* | -link) | ||
;; | ||
-lkernel32) | ||
# Ignore this library only on Windows-like systems. | ||
-- | ||
cgit v1.2.3-70-g09d2 | ||
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||
|
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38 changes: 38 additions & 0 deletions
38
easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb
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# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2 | ||
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easyblock = 'Tarball' | ||
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name = 'annovar' | ||
version = '20200607' # version reported by `annotate_variation.pl -h` | ||
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homepage = 'http://annovar.openbioinformatics.org/en/latest/' | ||
description = """ANNOVAR is an efficient software tool to utilize update-to-date information | ||
to functionally annotate genetic variants detected from diverse genomes (including human | ||
genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" | ||
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toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
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download_instructions = """ | ||
Registration required for download | ||
via http://www.openbioinformatics.org/annovar/annovar_download_form.php | ||
rename after download to %(name)s-%(version)s.tar.gz | ||
""" | ||
sources = ['%(name)s-%(version)s.tar.gz'] | ||
checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] | ||
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dependencies = [('Perl', '5.36.1')] | ||
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modextrapaths = {'PATH': ''} | ||
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sanity_check_paths = { | ||
'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", | ||
"variants_reduction.pl", "table_annovar.pl"], | ||
'dirs': ["example", "humandb"], | ||
} | ||
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sanity_check_commands = [ | ||
"annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), | ||
'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', | ||
] | ||
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moduleclass = 'bio' |
39 changes: 39 additions & 0 deletions
39
easybuild/easyconfigs/a/arrow-R/arrow-R-17.0.0.1-foss-2024a-R-4.4.2.eb
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easyblock = 'RPackage' | ||
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name = 'arrow-R' | ||
version = '17.0.0.1' | ||
versionsuffix = '-R-%(rver)s' | ||
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homepage = 'https://cran.r-project.org/web/packages/arrow' | ||
description = "R interface to the Apache Arrow C++ library" | ||
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toolchain = {'name': 'foss', 'version': '2024a'} | ||
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source_urls = [ | ||
'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive | ||
'https://cran.r-project.org/src/contrib/', # current version of packages | ||
'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages | ||
] | ||
sources = ['arrow_%(version)s.tar.gz'] | ||
checksums = ['0214dbf5d958968172a6f67abbae916d33933625cf41dc22e89ab77a29cde75e'] | ||
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builddependencies = [ | ||
('pkgconf', '2.2.0'), | ||
] | ||
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dependencies = [ | ||
('R', '4.4.2'), | ||
('R-bundle-CRAN', '2024.11'), | ||
('Arrow', '17.0.0'), # arrow-R x.y.z[.N] only works with Arrow x.y.z | ||
] | ||
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preinstallopts = "export LIBARROW_BUILD=false && " | ||
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sanity_check_paths = { | ||
'files': [], | ||
'dirs': ['arrow'], | ||
} | ||
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options = {'modulename': 'arrow'} | ||
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moduleclass = 'tools' |
40 changes: 40 additions & 0 deletions
40
easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0-CUDA-12.1.1.eb
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easyblock = 'Tarball' | ||
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name = 'Beast' | ||
version = '2.7.7' | ||
versionsuffix = '-CUDA-%(cudaver)s' | ||
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homepage = 'https://beast2.org' | ||
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular | ||
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using | ||
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies | ||
but is also a framework for testing evolutionary hypotheses without conditioning on a single | ||
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted | ||
proportional to its posterior probability. """ | ||
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toolchain = {'name': 'GCC', 'version': '12.3.0'} | ||
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_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} | ||
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source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] | ||
sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] | ||
checksums = [{ | ||
'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a', | ||
'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e', | ||
}] | ||
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dependencies = [ | ||
('CUDA', '12.1.1', '', SYSTEM), | ||
('Java', '11', '', SYSTEM), | ||
('beagle-lib', '4.0.1', versionsuffix), # optional but recommended by developers | ||
('GTK3', '3.24.37'), # optional for GUI tools | ||
] | ||
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sanity_check_paths = { | ||
'files': ['bin/beast'], | ||
'dirs': [] | ||
} | ||
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sanity_check_commands = ["beast -help"] | ||
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moduleclass = 'bio' |
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easyblock = 'Tarball' | ||
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name = 'Beast' | ||
version = '2.7.7' | ||
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homepage = 'https://beast2.org' | ||
description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular | ||
sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using | ||
strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies | ||
but is also a framework for testing evolutionary hypotheses without conditioning on a single | ||
tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted | ||
proportional to its posterior probability. """ | ||
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toolchain = {'name': 'GCC', 'version': '12.3.0'} | ||
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_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} | ||
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source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] | ||
sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] | ||
checksums = [{ | ||
'BEAST.v2.7.7.Linux.x86.tgz': 'a866f3e5da4ef890a042f01849e32322aa0a8e16e3e1cb2c59f823de2611781a', | ||
'BEAST.v2.7.7.Linux.aarch64.tgz': 'aa14e4a950fe2d9f3db24102a4e7365d8d42f79da1d9b1cdcf3016e927d18b9e', | ||
}] | ||
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dependencies = [ | ||
('Java', '11', '', SYSTEM), | ||
('beagle-lib', '4.0.1'), # optional but recommended by developers | ||
('GTK3', '3.24.37'), # optional for GUI tools | ||
] | ||
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sanity_check_paths = { | ||
'files': ['bin/beast'], | ||
'dirs': [] | ||
} | ||
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sanity_check_commands = ["beast -help"] | ||
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moduleclass = 'bio' |
31 changes: 31 additions & 0 deletions
31
easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb
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easyblock = 'PythonBundle' | ||
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name = 'Biotite' | ||
version = '0.41.0' | ||
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homepage = 'https://www.biotite-python.org/' | ||
description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to | ||
identify homologous sequence regions in a protein family or you would like to | ||
find disulfide bonds in a protein structure: Biotite has the right tool for | ||
you. This package bundles popular tasks in computational molecular biology into | ||
a uniform Python library.""" | ||
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toolchain = {'name': 'foss', 'version': '2022a'} | ||
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dependencies = [ | ||
('Python', '3.10.4'), | ||
('SciPy-bundle', '2022.05'), | ||
('networkx', '2.8.4'), | ||
] | ||
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use_pip = True | ||
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exts_list = [ | ||
('biotite', version, { | ||
'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], | ||
}), | ||
] | ||
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sanity_pip_check = True | ||
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moduleclass = 'bio' |
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