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…asyconfigs into 20250114105723_new_pr_dssp4410
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smoors committed Jan 22, 2025
2 parents bd91741 + cc1587b commit f6b9d71
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Expand Up @@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she
toolchain = {'name': 'GCCcore', 'version': '10.3.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_XZ]
checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4']
sources = [SOURCELOWER_TAR_GZ]
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.36.1'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.37'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.38'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.39'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.40'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.40'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.40'),
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@@ -0,0 +1,29 @@
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

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(-)

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


8 changes: 6 additions & 2 deletions easybuild/easyconfigs/a/Autoconf/Autoconf-2.71.eb
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Expand Up @@ -16,8 +16,12 @@ description = """Autoconf is an extensible package of M4 macros that produce she
toolchain = SYSTEM

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_XZ]
checksums = ['f14c83cfebcc9427f2c3cea7258bd90df972d92eb26752da4ddad81c87a0faa4']
sources = [SOURCELOWER_TAR_GZ]
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c', # autoconf-2.71.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

dependencies = [('M4', '1.4.18')]

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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '13.3.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e', # autoconf-2.72.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.42'),
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Expand Up @@ -18,7 +18,11 @@ toolchain = {'name': 'GCCcore', 'version': '14.2.0'}

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e']
patches = ['Autoconf-2.71-Port-better-to-NVHPC.patch']
checksums = [
'afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e', # autoconf-2.72.tar.gz
'157453a2f74821b06d3f7cd1ba8d2622f12d9e6d172a01e3ff8e8d32b3d7bfeb', # Autoconf-2.71-Port-better-to-NVHPC.patch
]

builddependencies = [
('binutils', '2.42'),
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38 changes: 38 additions & 0 deletions easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb
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@@ -0,0 +1,38 @@
# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2

easyblock = 'Tarball'

name = 'annovar'
version = '20200607' # version reported by `annotate_variation.pl -h`

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)."""

toolchain = {'name': 'GCCcore', 'version': '12.3.0'}

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']

dependencies = [('Perl', '5.36.1')]

modextrapaths = {'PATH': ''}

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"],
}

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"',
]

moduleclass = 'bio'
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@@ -0,0 +1,39 @@
easyblock = 'RPackage'

name = 'arrow-R'
version = '17.0.0.1'
versionsuffix = '-R-%(rver)s'

homepage = 'https://cran.r-project.org/web/packages/arrow'
description = "R interface to the Apache Arrow C++ library"

toolchain = {'name': 'foss', 'version': '2024a'}

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']

builddependencies = [
('pkgconf', '2.2.0'),
]

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
]

preinstallopts = "export LIBARROW_BUILD=false && "

sanity_check_paths = {
'files': [],
'dirs': ['arrow'],
}

options = {'modulename': 'arrow'}

moduleclass = 'tools'
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@@ -0,0 +1,40 @@
easyblock = 'Tarball'

name = 'Beast'
version = '2.7.7'
versionsuffix = '-CUDA-%(cudaver)s'

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. """

toolchain = {'name': 'GCC', 'version': '12.3.0'}

_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'}

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',
}]

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
]

sanity_check_paths = {
'files': ['bin/beast'],
'dirs': []
}

sanity_check_commands = ["beast -help"]

moduleclass = 'bio'
38 changes: 38 additions & 0 deletions easybuild/easyconfigs/b/Beast/Beast-2.7.7-GCC-12.3.0.eb
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@@ -0,0 +1,38 @@
easyblock = 'Tarball'

name = 'Beast'
version = '2.7.7'

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. """

toolchain = {'name': 'GCC', 'version': '12.3.0'}

_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'}

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',
}]

dependencies = [
('Java', '11', '', SYSTEM),
('beagle-lib', '4.0.1'), # optional but recommended by developers
('GTK3', '3.24.37'), # optional for GUI tools
]

sanity_check_paths = {
'files': ['bin/beast'],
'dirs': []
}

sanity_check_commands = ["beast -help"]

moduleclass = 'bio'
31 changes: 31 additions & 0 deletions easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-foss-2022a.eb
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@@ -0,0 +1,31 @@
easyblock = 'PythonBundle'

name = 'Biotite'
version = '0.41.0'

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."""

toolchain = {'name': 'foss', 'version': '2022a'}

dependencies = [
('Python', '3.10.4'),
('SciPy-bundle', '2022.05'),
('networkx', '2.8.4'),
]

use_pip = True

exts_list = [
('biotite', version, {
'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'],
}),
]

sanity_pip_check = True

moduleclass = 'bio'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
toolchain = {'name': 'GCC', 'version': '12.2.0'}
toolchainopts = {'pic': True}

source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
source_urls = ['https://archives.boost.io/release/%(version)s/source/']
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6']

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb
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Expand Up @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
toolchain = {'name': 'GCC', 'version': '12.3.0'}
toolchainopts = {'pic': True}

source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
source_urls = ['https://archives.boost.io/release/%(version)s/source/']
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c']

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Boost/Boost-1.83.0-GCC-13.2.0.eb
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
toolchain = {'name': 'GCC', 'version': '13.2.0'}
toolchainopts = {'pic': True}

source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
source_urls = ['https://archives.boost.io/release/%(version)s/source/']
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628']

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Boost/Boost-1.85.0-GCC-13.3.0.eb
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ description = """Boost provides free peer-reviewed portable C++ source libraries
toolchain = {'name': 'GCC', 'version': '13.3.0'}
toolchainopts = {'pic': True}

source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
source_urls = ['https://archives.boost.io/release/%(version)s/source/']
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
patches = ['Boost-1.85.0_fix-ppc-charconv.patch']
checksums = [
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