Merge branch 'easybuilders:develop' into 20241124161403_new_pr_R442

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'

easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb → 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'
 

easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb

@@ -0,0 +1,33 @@
+# author: Jillian Rowe <[email protected]>
+# config upgrade to v5.1.0 by Adam Huffman <[email protected]>
+# 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 <[email protected]>
+# config upgrade to 2019.03 by Davide Vanzo <[email protected]>
+# config upgrade to 2023.09 by Sarah Walters <[email protected]>
+
+# 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'

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'

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 <[email protected]>, 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'

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 <[email protected]>, Fotis Georgatos <[email protected]>
+# 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'

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'

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'),
 ]
 

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'