diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb new file mode 100644 index 00000000000..3e980962ec8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'ABRicate' +version = '1.0.0' + +homepage = 'https://github.com/tseemann/abricate' +description = "Mass screening of contigs for antimicrobial and virulence genes" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# https://github.com/tseemann/abricate +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] + +dependencies = [ + ('Perl', '5.38.0'), + ('any2fasta', '0.4.2'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), +] + +postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] + +sanity_check_paths = { + 'files': ['bin/abricate', 'bin/abricate-get_db'], + 'dirs': ['db'], +} + +sanity_check_commands = [ + "abricate --help", + "abricate --list", +] + +modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb similarity index 95% rename from easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb rename to easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb index 333a0374279..e614536bfb5 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('binutils', '2.42')] -dependencies = [('Java', '21.0.2', '', SYSTEM)] +dependencies = [('Java', '17', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb new file mode 100644 index 00000000000..674a7cc8fd6 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb @@ -0,0 +1,33 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10, 2024.2-1 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +# config upgrade to 2023.09 by Sarah Walters + +# no support for power architecture in 2024.02-1 on https://repo.anaconda.com/archive/, as off 13 Feb 2024 +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2024.06-1' + +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. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '539bb43d9a52d758d0fdfa1b1b049920ec6f8c6d15ee9fe4a423355fe551a8f7', + '%(name)s-%(version)s-Linux-aarch64.sh': 'b4be0ad2052236882402902a31d32cd37635d3db194a42f977be0d68a8ff1a31', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..91034a25be8 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.38.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb new file mode 100644 index 00000000000..d43cb118efd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb @@ -0,0 +1,58 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.16.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b'] + +builddependencies = [('cpio', '2.15')] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('PCRE', '8.45'), + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LMDB', '0.9.31'), + ('SQLite', '3.43.1'), +] + +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d65b73e57e9 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# 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 +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +# +# 0.7.18 +# Erica Bianco (HPCNow!) +## + +name = 'BWA' +version = '0.7.18' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..6cc5d76a73d --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,94 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0', versionsuffix), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25', versionsuffix), + ('dm-haiku', '0.0.12', versionsuffix), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2', versionsuffix), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('Flax', '0.8.4', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb index 49345e486d8..fd6186d58ec 100644 --- a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -30,7 +34,6 @@ dependencies = [ ('Optax', '0.2.2'), ('py3Dmol', '2.1.0'), ('JupyterLab', '4.0.5'), - ('hatchling', '1.18.0'), ('Flax', '0.8.4'), ] diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..8c8af50568f --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..b26850e9d30 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.38.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..85e6f82cb90 --- /dev/null +++ b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'bin2cell' +version = '0.3.2' + +homepage = 'https://github.com/Teichlab/bin2cell' +description = """Bin2cell proposes 2um bin to cell groupings based on segmentation, +which can be done on the morphology image and/or a visualisation of the gene expression.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scanpy', '1.9.8'), + ('OpenCV', '4.8.1', '-contrib'), + ('stardist', '0.8.5'), + ('fastparquet', '2024.11.0'), +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + (name, version, { + # opencv-python is installed via OpenCV, python module name is 'cv2' + 'preinstallopts': "sed -i '/opencv-python/d' pyproject.toml &&", + 'checksums': ['6529a8260b75c8c0237938f4ea389dfe055aea0909a31315f8fec32d44b2c531'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['python -c "import cv2"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index 5711e31168d..567ceb13c55 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '21.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index bb993fb6e99..81a314f451b 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '24.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB diff --git a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb index 355a9996fbc..f4b0e614fd7 100644 --- a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb @@ -25,6 +25,7 @@ builddependencies = [ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('LibTIFF', '4.5.0'), + ('librsvg', '2.58.0'), ] _bins = ['bin/%s' % x for x in ['any2djvu', 'bzz', 'c44', 'cjb2', 'cpaldjvu', 'csepdjvu', 'ddjvu', 'djvm', 'djvmcvt', diff --git a/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a215ceeed07 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "1.1.0" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry', '1.6.1') +] + +dependencies = [ + ('git-annex', '10.20240531'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('tqdm', '4.66.2'), + ('PLY', '3.11'), + ('scikit-build', '0.17.6'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('patool', '2.3.0', { + 'modulename': 'patoolib', + 'checksums': ['498e294fd8c7d50889d65019d431c6867bf3fb1fec5ea2d39d1d39d1215002f8'], + }), + ('annexremote', '1.6.5', { + 'checksums': ['ad0ccdd84a8771ad58922d172ee68b225ece77bf464abe4d24ff91a4896a423e'], + }), + ('looseversion', '1.3.0', { + 'checksums': ['ebde65f3f6bb9531a81016c6fef3eb95a61181adc47b7f949e9c0ea47911669e'], + }), + ('botocore', '1.34.121', { + 'checksums': ['1a8f94b917c47dfd84a0b531ab607dc53570efb0d073d8686600f2d2be985323'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.2', { + 'checksums': ['0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6'], + }), + ('boto3', '1.34.121', { + 'checksums': ['ec89f3e0b0dc959c418df29e14d3748c0b05ab7acf7c0b90c839e9f340a659fa'], + }), + ('python_gitlab', '4.5.0', { + 'modulename': 'gitlab', + 'checksums': ['0a106174949819912b9abb4232e39059f83f613177fdb1787097eb84481c64b2'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + (name, version, { + 'checksums': ['3403232696ae0e6cbcec56d7cccfac1be8b5d98f66f235e4751dd44fd9f5e8eb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb new file mode 100644 index 00000000000..6724da1d7f8 --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -0,0 +1,251 @@ +easyblock = 'CargoPythonBundle' + +name = 'fastparquet' +version = '2024.11.0' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming to integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('NASM', '2.16.01'), +] + +crates = [ + ('adler2', '2.0.0'), + ('alloc-no-stdlib', '2.0.4'), + ('alloc-stdlib', '0.2.2'), + ('atty', '0.2.14'), + ('autocfg', '1.4.0'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('blosc2-rs', '0.3.1+2.15.1'), + ('blosc2-sys', '0.3.1+2.15.1'), + ('brotli', '7.0.0'), + ('brotli-decompressor', '4.0.1'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cbindgen', '0.24.5'), + ('cc', '1.1.30'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('copy_dir', '0.1.3'), + ('crc32fast', '1.4.2'), + ('errno', '0.3.9'), + ('fastrand', '2.1.1'), + 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('python3-dll-a', '0.2.10'), + ('quote', '1.0.37'), + ('redox_syscall', '0.5.7'), + ('rustix', '0.38.37'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('serde_json', '1.0.128'), + ('shlex', '1.3.0'), + ('smallvec', '1.13.2'), + ('snap', '1.1.1'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.13.0'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('toml', '0.5.11'), + ('unicode-ident', '1.0.13'), + ('unindent', '0.2.3'), + ('walkdir', '2.5.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), + ('zstd', '0.13.2'), + ('zstd-safe', '7.2.1'), + ('zstd-sys', '2.0.13+zstd.1.5.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('thrift', '0.21.0', { + 'checksums': ['5e6f7c50f936ebfa23e924229afc95eb219f8c8e5a83202dd4a391244803e402'], + }), + ('cramjam', '2.9.0', { + 'checksums': ['f103e648aa3ebe9b8e2c1a3a92719288d8f3f41007c319ad298cdce2d0c28641'], + }), + (name, version, { + 'checksums': ['e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'], + }), +] + +checksums = [ + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'}, + {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'}, + 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'8acb788b847c24f28525660c4d7758620a7210875711f79e7f663cc152726811'}, + {'ryu-1.0.18.tar.gz': 'f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f'}, + {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'serde-1.0.210.tar.gz': 'c8e3592472072e6e22e0a54d5904d9febf8508f65fb8552499a1abc7d1078c3a'}, + {'serde_derive-1.0.210.tar.gz': '243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f'}, + {'serde_json-1.0.128.tar.gz': '6ff5456707a1de34e7e37f2a6fd3d3f808c318259cbd01ab6377795054b483d8'}, + {'shlex-1.3.0.tar.gz': '0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64'}, + {'smallvec-1.13.2.tar.gz': '3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67'}, + {'snap-1.1.1.tar.gz': '1b6b67fb9a61334225b5b790716f609cd58395f895b3fe8b328786812a40bc3b'}, + {'strsim-0.10.0.tar.gz': '73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.79.tar.gz': '89132cd0bf050864e1d38dc3bbc07a0eb8e7530af26344d3d2bbbef83499f590'}, + {'target-lexicon-0.12.16.tar.gz': '61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1'}, + {'tempfile-3.13.0.tar.gz': 'f0f2c9fc62d0beef6951ccffd757e241266a2c833136efbe35af6cd2567dca5b'}, + {'termcolor-1.4.1.tar.gz': '06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755'}, + {'textwrap-0.16.1.tar.gz': '23d434d3f8967a09480fb04132ebe0a3e088c173e6d0ee7897abbdf4eab0f8b9'}, + {'toml-0.5.11.tar.gz': 'f4f7f0dd8d50a853a531c426359045b1998f04219d88799810762cd4ad314234'}, + {'unicode-ident-1.0.13.tar.gz': 'e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb new file mode 100644 index 00000000000..7edbb913770 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'GPAW-setups' +version = '24.11.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """PAW setups for the GPAW Density Functional Theory package. +Users can install setups manually using 'gpaw install-data' or use setups from this package. +The versions of GPAW and GPAW-setups can be intermixed. + +Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, +which can be manually selected. Otherwise no changes are made, so no results will change. + +Version 21.11.0 contains setups for the Lanthanides. +""" + +toolchain = SYSTEM +source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['964c81cc28f7f91a4686d3d3182c4ebda30efb09d3f96b7f95eae3146499c110'] + +modextrapaths = {'GPAW_SETUP_PATH': ''} + +moduleclass = 'chem' + +sanity_check_paths = { + 'files': ['H.LDA.gz'], + 'dirs': [] +} diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b677adb6a37 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,63 @@ +name = 'Gurobi' +version = '12.0.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'} +sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi12.0.0_linux64.tar.gz': 'a2bdc9c1d6bf8eb4e551a184af1ce8d7b0435ea8e7d19a017cc7d53fd5efda12', + 'gurobi12.0.0_armlinux64.tar.gz': '8e1202cbf0866a16fa78c3e4be0fa32888ec912f8ddf333c29561d057964ef86'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', version, { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + 'fc3892e3d88d0f8a01da75f12f74023d398ef599a9e1add66ed76313733e30fb', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + 'a08fb42a5e7cb02cdb993c1381c8b8c5a3baeedcadd56e7288d8458a57b81442', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8ff1261cea3 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240531' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.42.0'), + ('libnsl', '2.0.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..83d24a82eec --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +builddependencies = [('binutils', '2.40')] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb new file mode 100644 index 00000000000..9a2bc1d7398 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.19.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['e7d7803cab4e12e84f5359a3d73915a45acc6d676151ca18e91fb2d39432b568'] + +dependencies = [('Java', '17', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb index 7640cb6a545..b7fbebbccca 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.11' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb index 9d6371e84ba..7d6d8ec7ec1 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.15' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb index 647d345e73e..3cf9fb88dc9 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.20.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb index 38d6c4a7d6e..e2065d805b0 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.22.1')] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb similarity index 89% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb index bb5cb6bf57c..93f14603ac1 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb @@ -6,14 +6,16 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb similarity index 90% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb index cf871e99182..164821bc84e 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb @@ -6,14 +6,16 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb similarity index 90% rename from easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb index 9d966d5571b..c0a02db1292 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb @@ -8,14 +8,16 @@ version = '1.16.2' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb similarity index 90% rename from easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb index ee355100089..9ca2db177a2 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb @@ -8,14 +8,16 @@ version = '1.17.6' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d71707d2105 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libtirpc', '1.3.4'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..b0262f35599 --- /dev/null +++ b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' + +name = 'MitoFinder' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/RemiAllio/MitoFinder' +description = """MitoFinder is a pipeline to assemble mitochondrial genomes and +annotate mitochondrial genes from trimmed read sequencing data""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/RemiAllio/MitoFinder/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2d6d3925fb014777df97f272134143cc518944ae05d000a44ada2862d46ec95a'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '2.7.18'), + ('IDBA-UD', '1.1.3'), + ('Infernal', '1.1.5'), + ('tRNAscan-SE', '2.0.12'), + ('Automake', '1.16.5'), +] + +postinstallcmds = [ + # avoid run install.sh + link EB modules + "rm -rf %(installdir)s/idba/bin && cd %(installdir)s/idba && ln -s $EBROOTIDBAMINUD/bin && " + "cd %(installdir)s/metaspades/bin && ln -s spades.py metaspades.py && " + "cd %(installdir)s/trnascanSE && mkdir -p infernal-1.1.3/exec && cd infernal-1.1.3/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/trnascanSE && mkdir -p automake-1.13.4/exec && cd automake-1.13.4/exec && " + "ln -s $EBROOTAUTOMAKE/bin && ln -s $EBROOTAUTOMAKE/share && " + "cd %(installdir)s/trnascanSE && mkdir -p tRNAscan-SE-2.0/exec && cd tRNAscan-SE-2.0/exec && " + "ln -s $EBROOTTRNASCANMINSE/bin && ln -s $EBROOTTRNASCANMINSE/lib && ln -s $EBROOTTRNASCANMINSE/include && " + "cd %(installdir)s/mitfi && mkdir -p infernal-1.0.2/exec && cd infernal-1.0.2/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/mitfi/infernal-1.0.2 && ln -s $EBROOTINFERNAL/bin src && " + 'cd %(installdir)s && touch install.sh.ok && ' + # fix mitofinder - https://github.com/RemiAllio/MitoFinder/issues/26 + "sed -i 's/os.devnull, \'wb\')/os.devnull, \'wb\'), shell=True/g' mitofinder" +] + +fix_python_shebang_for = ['mitofinder', '*.py'] + +sanity_check_paths = { + 'files': ['mitofinder'], + 'dirs': ['idba', 'megahit', 'metaspades', 'mitfi', 'trnascanSE'], +} + +sanity_check_commands = ['mitofinder -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb index cf83d365785..b0a8726462e 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb @@ -4,7 +4,7 @@ name = 'NCO' version = '5.2.9' homepage = "https://github.com/nco/nco" -description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.""" toolchain = {'name': 'foss', 'version': '2024a'} @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('UDUNITS', '2.2.28'), ('expat', '2.6.2'), - ('ANTLR', '2.7.7', '-Java-21.0.2'), + ('ANTLR', '2.7.7', '-Java-17'), ('libdap', '3.21.0-131'), ('GSL', '2.8'), ('netCDF', '4.9.2'), diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb index d7e1c6cc2e0..985e8ad0158 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -179,6 +179,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb index 4c8d8ef847a..50a7708dfa0 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb @@ -176,6 +176,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb new file mode 100644 index 00000000000..2e84effbc53 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.14.1'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20230722'), + ('tbl2asn', '20230713'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb new file mode 100644 index 00000000000..bd7648a5418 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20240322'), + ('tbl2asn', '20230713'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb new file mode 100644 index 00000000000..5baecf1ad17 --- /dev/null +++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'SKESA' +version = '2.4.0' +versionsuffix = '_saute.1.3.0_2' + +homepage = 'https://github.com/ncbi/SKESA' +description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs." + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/ncbi/SKESA/archive/'] +sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979'] + +dependencies = [ + ('Boost', '1.83.0'), + ('SRA-Toolkit', '3.1.1'), + ('ncbi-vdb', '3.1.1'), +] + +prebuildopts = "touch %(builddir)s/ngs.done && " + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" ' +buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB" + +files_to_copy = [(['skesa'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skesa'], + 'dirs': [], +} + +sanity_check_commands = ["skesa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b164481d03e --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'SMV' # SmokeView +version = '6.9.5' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/firemodels/smv/archive/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6c6203f6d6cd83c3525c7447ce4201c8df373d18d0c992d607ad232a77590ef7'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] +dependencies = [ + ('libgd', '2.3.3'), + ('freeglut', '3.4.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('json-c', '0.16'), + ('Doxygen', '1.9.7'), + ('glew', '2.2.0', '-osmesa'), +] + +configopts = '-DVERIFICATION_TESTS=ON' + +sanity_check_commands = [ + 'smokediff -h', + 'smokezip -h', + 'smvq -h', + 'smokeview -h 2>&1 | grep "Visualize"', +] + +sanity_check_paths = { + 'files': ['bin/smokeview', 'bin/smokediff', 'bin/smokezip', 'bin/smvq'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb index 50ead1b54c1..ddaa26cbca6 100644 --- a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -139,6 +139,120 @@ crates = [ ('zerocopy-derive', '0.7.35'), ] +checksums = [ + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anes-0.1.6.tar.gz': 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'1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] use_pip = True diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb new file mode 100644 index 00000000000..de10882b67d --- /dev/null +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'stardist' +version = '0.8.5' + +homepage = 'https://github.com/stardist/stardist' +description = "Object Detection with Star-convex Shapes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['260a31df86ca711e5e98cb91597c6cb9a10dcd1dc3c6b826d41b7c73c9646a1e'] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('numba', '0.58.1'), + ('scikit-image', '0.22.0'), + ('imageio', '2.33.1'), + ('CSBDeep', '0.7.4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "stardist-predict2d --help", + "stardist-predict3d --help", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3571e61aac4 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb @@ -0,0 +1,69 @@ +# 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 +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb new file mode 100644 index 00000000000..3a4edc7bc1c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = 'https://vcftools.github.io' +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = '%(namelower)s' +source_urls = [GITHUB_LOWER_RELEASE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), + ('HTSlib', '1.19.1'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/vcf-sort', 'bin/vcf-stats'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..389aac870e5 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WPS' +version = '4.6.0' + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', + 'WPS-4.6.0_fix_jasper_decode.patch', +] + +checksums = [ + 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz + 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch + 'f4ea3c77c42c3474d582e311b8bd0d80c67243f45922e85ee3ff52df61d6c77e', # WPS-4.6.0_fix_jasper_decode.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.38.2'), +] + +dependencies = [ + ('WRF', '4.6.1', versionsuffix), + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch new file mode 100644 index 00000000000..4f6d416931f --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch @@ -0,0 +1,31 @@ +# Using correct JasPer functions +# ============================== +# WPS uses depreceated version of JasPer interface. +# See https://github.com/wrf-model/WPS/issues/207 +# @author Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:58:34.322941000 +0100 +@@ -80,7 +80,7 @@ + /* + * Decode JPEG200 codestream into jas_image_t structure. + */ +- image=jpc_decode(jpcstream,opts); ++ image=jas_image_decode(jpcstream,jas_image_getfmt(jpcstream),opts); + if ( image == 0 ) { + printf(" jpc_decode return = %d \n",ier); + return -3; +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:58:40.467583000 +0100 +@@ -178,7 +178,7 @@ + /* + * Encode image. + */ +- ier=jpc_encode(&image,jpcstream,opts); ++ ier=jas_image_encode(&image,jpcstream,opts); + if ( ier != 0 ) { + printf(" jpc_encode return = %d \n",ier); + return -3; diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..098eed8d7fe --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,51 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# updated for WPS v4.6.0 by Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/arch/preamble WPS-4.6.0/arch/preamble +--- WPS-4.6.0.orig/arch/preamble 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/arch/preamble 2024-11-29 09:25:27.634254674 +0100 +@@ -39,13 +39,14 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include \ ++ -I$(NETCDFF_DIR)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ + -L$(WRF_DIR)/external/io_int -lwrfio_int \ + -L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \ +- -L$(NETCDF)/lib CONFIGURE_NETCDFF_LIB -lnetcdf ++ -L$(NETCDF)/lib -L$(NETCDFF_DIR)/lib -lnetcdff -lnetcdf + + #### Architecture specific settings #### + +diff -Nru WPS-4.6.0.orig/configure WPS-4.6.0/configure +--- WPS-4.6.0.orig/configure 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/configure 2024-11-29 09:17:10.196985634 +0100 +@@ -161,7 +161,7 @@ + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available + NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then ++ if [ -f "$NETCDFF_DIR/lib/libnetcdff.a" ] ; then + NETCDFF="-lnetcdff" + fi + else +@@ -429,9 +429,9 @@ + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` + FORMAT_FREE=`grep ^FORMAT_FREE configure.wps | cut -d"=" -f2-` + FFLAGS=`printf "%s" "${FFLAGS}" | sed -e "s/\\$(FORMAT_FREE)/${FORMAT_FREE}/g"` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF_DIR/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -L${NETCDFF_DIR}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..82904273536 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -0,0 +1,45 @@ +name = 'WRF' +version = '4.6.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +github_account = 'wrf-model' +source_urls = [GITHUB_RELEASE] +sources = ['v%(version)s.tar.gz'] + +# WRF-4.5.1_netCDF-Fortran_separate_path.patch no longer required for version 4.5.2 + +checksums = [ + {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20231222'), + ('tcsh', '6.24.13'), + ('time', '1.9'), + ('Perl', '5.38.2'), +] + +dependencies = [ + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), +] + +preconfigopts = "export NETCDF=$EBROOTNETCDFMINFORTRAN && export NETCDF_C=$EBROOTNETCDF &&" + +runtest = True + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3cb03e7142a --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20240930' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), + ('FFmpeg', '6.0'), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'modulename': 'whisper', + 'checksums': ['b7178e9c1615576807a300024f4daa6353f7e1a815dac5e38c33f1ef055dd2d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai'