Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20241017135930_new_pr_Spyder601

easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.3.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Archive-Zip'
+version = '1.68'
+
+homepage = 'https://metacpan.org/pod/Archive::Zip'
+description = "Provide an interface to ZIP archive files."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('UnZip', '6.0'),
+    ('Zip', '3.0'),
+]
+
+options = {'modulename': 'Archive::Zip'}
+
+sanity_check_paths = {
+    'files': ['bin/crc32'],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/a/Autoconf/Autoconf-2.72-GCCcore-14.2.0.eb

@@ -0,0 +1,48 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.72'
+
+homepage = 'https://www.gnu.org/software/autoconf/'
+
+description = """
+ Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can
+ adapt the packages to many kinds of UNIX-like systems without manual user
+ intervention. Autoconf creates a configuration script for a package from a
+ template file that lists the operating system features that the package can
+ use, in the form of M4 macro calls.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['afb181a76e1ee72832f6581c0eddf8df032b83e2e0239ef79ebedc4467d92d6e']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+    # non-standard Perl modules are required,
+    # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822
+    ('Perl', '5.40.0'),
+]
+
+preconfigopts = "export PERL='/usr/bin/env perl' && "
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x
+              for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
+                        "autoscan", "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "autoconf --help",
+    "autom4te --help",
+]
+
+moduleclass = 'devel'

easybuild/easyconfigs/a/Automake/Automake-1.17-GCCcore-14.2.0.eb

@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = '1.17'
+
+homepage = 'https://www.gnu.org/software/automake/automake.html'
+
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['Automake-%(version)s_perl_env_space.patch']
+checksums = [
+    {'automake-1.17.tar.gz': '397767d4db3018dd4440825b60c64258b636eaf6bf99ac8b0897f06c89310acd'},
+    {'Automake-1.17_perl_env_space.patch': 'a416eeb854df009f0cdec0484282a3cf7ff6b2637a59e1188932d946625196ab'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Autoconf', '2.72'),
+    # non-standard Perl modules are required,
+    # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822
+    ('Perl', '5.40.0'),
+]
+
+preconfigopts = "export PERL='/usr/bin/env perl' && "
+
+sanity_check_paths = {
+    'files': ['bin/aclocal', 'bin/automake'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "aclocal --help",
+    "automake --help",
+]
+
+moduleclass = 'devel'

easybuild/easyconfigs/a/Automake/Automake-1.17_perl_env_space.patch

@@ -0,0 +1,19 @@
+Removes the incorrect assumption that the shebang must not have spaces,
+since we correctly use "/usr/bin/env perl"
+
+author: micketeer@gmail.com
+
+--- configure.orig	2024-12-08 14:41:01.243852603 +0000
++++ configure	2024-12-08 14:41:51.837762787 +0000
+@@ -3513,11 +3513,6 @@
+  '')
+    as_fn_error $? "perl not found" "$LINENO" 5
+    ;;
+- *' '* | *'	'*)
+-  as_fn_error $? "The path to your Perl contains spaces or tabs.
+-This would cause build failures later or unusable programs.
+-Please use a path without spaces and try again." "$LINENO" 5
+-  ;;
+ esac
+
+ # Save details about the selected perl interpreter in config.log.

easybuild/easyconfigs/a/Autotools/Autotools-20240712-GCCcore-14.2.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20240712'  # date of the most recent change
+
+homepage = 'https://autotools.io'
+
+description = """
+ This bundle collect the standard GNU build tools: Autoconf, Automake
+ and libtool
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+
+dependencies = [
+    ('Autoconf', '2.72'),    # 20240712
+    ('Automake', '1.17'),    # 20211003
+    ('libtool', '2.5.4'),    # 20220317
+]
+
+# Pure bundle -- no need to specify 'binutils' used when building GCCcore
+# toolchain as build dependency
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2023b.eb

@@ -0,0 +1,41 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# updated: Denis Kristak (INUITS)
+# Update: Petr Král (INUITS)
+
+easyblock = 'MakeCp'
+
+name = 'BEDOPS'
+version = '2.4.41'
+
+homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html'
+description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and
+ scalable Boolean and other set operations, statistical calculations, archiving, conversion and
+ other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for
+ distributing whole-genome analyses across a computational cluster."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194']
+
+# else build of jansson library fails with: 'configure: error: C compiler cannot create executables'
+prebuildopts = 'unset LIBS && '
+# builds all variants and copies executables to bin directory
+buildopts = ' all && make install'
+# actually used variant is linked to via symlinks
+keepsymlinks = True
+
+files_to_copy = ['bin']
+
+sanity_check_paths = {
+    'files': [
+        'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch']
+    ],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.3.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-DB-HTS'
+version = '3.01'
+
+homepage = 'https://metacpan.org/release/Bio-DB-HTS'
+description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/']
+sources = ['Bio-DB-HTS-%(version)s.tar.gz']
+checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42']
+
+builddependencies = [('pkgconf', '1.9.5')]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('BioPerl', '1.7.8'),
+    ('HTSlib', '1.18'),
+]
+
+preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"
+
+options = {'modulename': 'Bio::DB::HTS'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb

@@ -0,0 +1,58 @@
+# easybuild easyconfig
+#
+#  John Dey jfdey@fredhutch.org
+#
+#  Fred Hutchinson Cancer Research Center
+#  Thomas Eylenbosch - Gluo NV 
+
+easyblock = 'Bundle'
+
+name = 'BioPerl'
+version = '1.7.8'
+
+homepage = 'https://bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
+    ('XML-LibXML', '2.0210'),
+    ('DB_File', '1.859'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('XML::Writer', '0.900', {
+        'source_tmpl': 'XML-Writer-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'],
+        'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'],
+    }),
+    ('Bio::Procedural', '1.7.4', {
+        'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.213-GCCcore-12.3.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'PerlModule'
+
+name = 'Compress-Raw-Zlib'
+version = '2.213'
+
+homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib'
+description = "Low-Level Interface to zlib or zlib-ng compression library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['56b21c99cb3a3a7f7876a74dd05daa3f41fc9143ddd4dc98f8e46710a106af45']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('zlib', '1.2.13'),
+]
+
+options = {'modulename': 'Compress::Raw::Zlib'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb

@@ -0,0 +1,33 @@
+name = 'DB'
+version = '18.1.40'
+
+homepage = 'https://www.oracle.com/technetwork/products/berkeleydb'
+
+description = """Berkeley DB enables the development of custom data management
+ solutions, without the overhead traditionally associated with such custom
+ projects."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+# use http to allow auto-downloading...
+source_urls = ['http://download.oracle.com/berkeley-db/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix_doc_install.patch']
+checksums = [
+    '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8',  # db-18.1.40.tar.gz
+    '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
+]
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('OpenSSL', '1.1', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup',
+                                        'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat',
+                                        'tuner', 'upgrade', 'verify']] +
+             ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'