Merge branch '5.0.x' into cmake-libdir-clean

easybuild/easyconfigs/0/4ti2/4ti2-1.6.10-GCC-13.2.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = '4ti2'
+version = '1.6.10'
+
+homepage = 'https://4ti2.github.io/'
+description = """A software package for algebraic, geometric and combinatorial problems on linear spaces"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = '4ti2'
+source_urls = [GITHUB_SOURCE]
+sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['2f1bce3203da65b651d68cbd0ace0f89a16d1f436cf5f24e22bc15ec22df936a']
+
+dependencies = [
+    ('GMP', '6.3.0'),
+    ('GLPK', '5.0'),
+]
+
+builddependencies = [('Autotools', '20220317')]
+
+preconfigopts = './autogen.sh && '
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']],
+    'dirs': ['include/4ti2', 'lib', 'share']
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2023a.eb

@@ -0,0 +1,22 @@
+easyblock = 'PythonPackage'
+
+name = 'adjustText'
+version = '0.7.3'
+
+homepage = 'https://github.com/Phlya/adjustText'
+description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('matplotlib', '3.7.2'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+options = {'modulename': 'adjustText'}
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/aiohttp/aiohttp-3.9.5-GCCcore-13.2.0.eb

@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'aiohttp'
+version = '3.9.5'
+
+homepage = 'https://github.com/aio-libs/aiohttp'
+description = "Asynchronous HTTP client/server framework for asyncio and Python."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('poetry', '1.6.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+]
+
+# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies
+exts_list = [
+    ('multidict', '6.0.5', {
+        'checksums': ['f7e301075edaf50500f0b341543c41194d8df3ae5caf4702f2095f3ca73dd8da'],
+    }),
+    ('expandvars', '0.12.0', {
+        'checksums': ['7d1adfa55728cf4b5d812ece3d087703faea953e0c0a1a78415de9df5024d844'],
+    }),
+    ('yarl', '1.9.4', {
+        'checksums': ['566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf'],
+    }),
+    ('frozenlist', '1.4.1', {
+        'checksums': ['c037a86e8513059a2613aaba4d817bb90b9d9b6b69aace3ce9c877e8c8ed402b'],
+    }),
+    ('async-timeout', '4.0.3', {
+        'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'],
+    }),
+    ('aiosignal', '1.3.1', {
+        'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'],
+    }),
+    ('aiohappyeyeballs', '2.3.2', {
+        'checksums': ['77e15a733090547a1f5369a1287ddfc944bd30df0eb8993f585259c34b405f4e'],
+    }),
+    (name, version, {
+        'checksums': ['edea7d15772ceeb29db4aff55e482d4bcfb6ae160ce144f2682de02f6d693551'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/atropos/atropos-1.1.32-gompi-2023a.eb

@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'atropos'
+version = '1.1.32'
+
+homepage = 'https://atropos.readthedocs.io'
+description = "Atropos is tool for specific, sensitive, and speedy trimming of NGS reads."
+
+toolchain = {'name': 'gompi', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('tqdm', '4.66.1'),
+    ('Pysam', '0.22.0'),
+    ('pytest', '7.4.2'),
+    ('SRA-Toolkit', '3.0.10'),
+]
+
+exts_list = [
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('screed', '1.1.3', {
+        'checksums': ['37e81697c7dba95a053554e5b5a86aff329705e1cf5dfc5e7b8da586dee072b8'],
+    }),
+    ('bz2file', '0.98', {
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('khmer', '2.1.1', {
+        'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'],
+    }),
+    ('pokrok', '0.2.0', {
+        'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'],
+    }),
+    ('xphyle', '4.0.5', {
+        'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'],
+    }),
+    ('srastream', '0.1.3', {
+        'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'],
+    }),
+    (name, version, {
+        'checksums': ['17e9dc3d76d7a2ca607a12da191a6d7ba1cfbd1a8c924215870417f85858fd83'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/atropos'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["atropos detect --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb

@@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v
 sources = ['ncbi-blast-%(version)s+-src.tar.gz']
 checksums = ['89553714d133daf28c477f83d333794b3c62e4148408c072a1b4620e5ec4feb2']
 
+builddependencies = [('cpio', '2.14')]
+
 dependencies = [
     ('zlib', '1.2.12'),
     ('bzip2', '1.0.8'),

easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb

@@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v
 sources = ['ncbi-blast-%(version)s+-src.tar.gz']
 checksums = ['bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500']
 
+builddependencies = [('cpio', '2.15')]
+
 dependencies = [
     ('zlib', '1.2.12'),
     ('bzip2', '1.0.8'),

easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb

@@ -27,6 +27,8 @@ source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(v
 sources = ['ncbi-blast-%(version)s+-src.tar.gz']
 checksums = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e']
 
+builddependencies = [('cpio', '2.15')]
+
 dependencies = [
     ('zlib', '1.2.13'),
     ('bzip2', '1.0.8'),

easybuild/easyconfigs/b/BLIS/BLIS-1.0-GCC-13.3.0.eb

@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'BLIS'
+version = '1.0'
+
+homepage = 'https://github.com/flame/blis/'
+description = """BLIS is a portable software framework for instantiating high-performance
+BLAS-like dense linear algebra libraries."""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/flame/blis/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['9c12972aa1e50f64ca61684eba6828f2f3dd509384b1e41a1e8a9aedea4b16a6']
+
+builddependencies = [
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
+]
+
+configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['include/blis/cblas.h', 'include/blis/blis.h',
+              'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+modextrapaths = {'CPATH': 'include/blis'}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-12.3.0.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': '12.3.0'}
+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 = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+# 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/Boost/Boost-1.85.0-GCC-13.3.0.eb

@@ -0,0 +1,31 @@
+##
+# Authors::   Denis Kristak <[email protected]>
+##
+name = 'Boost'
+version = '1.85.0'
+
+homepage = 'https://www.boost.org/'
+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/']
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['be0d91732d5b0cc6fbb275c7939974457e79b54d6f07ce2e3dfdd68bef883b0b']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+    ('XZ', '5.4.5'),
+    ('zstd', '1.5.6'),
+    ('ICU', '75.1'),
+]
+
+configopts = '--without-libraries=python,mpi'
+
+# disable MPI, build Boost libraries with tagged layout
+boost_mpi = False
+tagged_layout = True
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'Brotli'
+version = '1.1.0'
+
+homepage = 'https://github.com/google/brotli'
+description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination
+ of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio
+ comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate
+ but offers more dense compression.
+The specification of the Brotli Compressed Data Format is defined in RFC 7932."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/google/brotli/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e720a6ca29428b803f4ad165371771f5398faba397edf6778837a18599ea13ff']
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["brotli --help"]
+
+moduleclass = 'lib'