{bio}[gompi/2023a] MEME v5.5.7, XML-Compile v1.63, XML-LibXML v2.0210

easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb

@@ -0,0 +1,63 @@
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'ConfigureMake'
+
+name = 'MEME'
+version = '5.5.7'
+
+homepage = 'https://meme-suite.org/meme/index.html'
+description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or
+ GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using
+ MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate
+ motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment
+ using SpaMo or CentriMo."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['1dca8d0e6d1d36570c1a88ab8dbe7e4b177733fbbeacaa2e8c4674febf57aaf4']
+
+dependencies = [
+    ('libxml2', '2.11.5'),
+    ('libxslt', '1.1.38'),
+    ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+    ('Python', '3.11.5'),
+    ('Ghostscript', '10.02.1'),
+    ('XML-Compile', '1.63'),
+]
+
+configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python '
+configopts += '--with-gs=${EBROOTGHOSTSCRIPT}/bin/gs '
+# config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl)
+configopts += " && grep 'All required and optional Perl modules were found' config.log"
+
+pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 "
+# test xstreme4 fails on Ubuntu 20.04, see: https://groups.google.com/g/meme-suite/c/GlfpGwApz1Y
+runtest = 'test'
+
+fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*']
+fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*']
+
+sanity_check_paths = {
+    'files': ['bin/meme', 'bin/dreme', 'bin/meme-chip', 'libexec/meme-%(version)s/meme2meme'],
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = [
+    "mpirun meme -h 2>&1 | grep 'Usage:'",
+    "meme2meme --help",
+    "perl -e 'require MemeSAX'",
+    "python -c 'import sequence_py3'",
+]
+
+modextrapaths = {
+    'PATH': ['libexec/meme-%(version)s'],
+    'PERL5LIB': ['lib/meme-%(version)s/perl'],
+    'PYTHONPATH': ['lib/meme-%(version)s/python'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb

@@ -0,0 +1,61 @@
+easyblock = 'Bundle'
+
+name = 'XML-Compile'
+version = '1.63'
+
+homepage = 'https://metacpan.org/pod/XML::Compile'
+description = "Perl module for compilation based XML processing"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('pkgconf', '2.0.3'),
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('XML-LibXML', '2.0210'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perl -e 'require %(ext_name)s'", '')
+
+exts_list = [
+    ('XML::LibXML::Simple', '1.01', {
+        'source_tmpl': 'XML-LibXML-Simple-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'],
+        'checksums': ['cd98c8104b70d7672bfa26b4513b78adf2b4b9220e586aa8beb1a508500365a6'],
+    }),
+    ('XML::Compile', version, {
+        'source_tmpl': 'XML-Compile-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'],
+        'checksums': ['4b0871ef4a70bff37266d531bebcd1d065b109e8f5c5e996f87189a9f92d595f'],
+    }),
+    ('XML::Compile::Cache', '1.06', {
+        'source_tmpl': 'XML-Compile-Cache-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'],
+        'checksums': ['591b136bd92842c81a5176082503f47df6d5cc4d8e0d78953ef1557f747038a0'],
+    }),
+    ('XML::Compile::SOAP', '3.28', {
+        'source_tmpl': 'XML-Compile-SOAP-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'],
+        'checksums': ['0921699c4522537f7930e14fac056492de7801a9b9140d0e1faf33414ae6998f'],
+    }),
+    ('XML::Compile::WSDL11', '3.08', {
+        'source_tmpl': 'XML-Compile-WSDL11-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'],
+        'checksums': ['dd687ccf5083fe98fce1dd18540e1d0175042437a986e33eec105eca248f8d42'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/XML/Compile'],
+}
+
+moduleclass = 'data'

easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb

@@ -0,0 +1,65 @@
+# updated toolchain, version, and dependency versions
+# Thomas Eylenbosch 5-Jun-23
+
+easyblock = 'Bundle'
+
+name = 'XML-LibXML'
+version = '2.0210'
+
+homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod'
+description = "Perl binding for libxml2"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
+    ('libxml2', '2.11.5'),
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('File::chdir', '0.1011', {
+        'source_tmpl': 'File-chdir-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'],
+        'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'],
+    }),
+    ('Alien::Base', '2.83', {
+        'source_tmpl': 'Alien-Build-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'],
+        'checksums': ['4817270314431350ff397125547f55641dcff98bdde213b9e5efc613f7c8b85a'],
+    }),
+    ('Alien::Build::Plugin::Download::GitLab', '0.01', {
+        'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'],
+    }),
+    ('Alien::Libxml2', '0.19', {
+        'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'],
+        'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'],
+    }),
+    ('XML::LibXML', version, {
+        'source_tmpl': 'XML-LibXML-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'],
+        'checksums': ['a29bf3f00ab9c9ee04218154e0afc8f799bf23674eb99c1a9ed4de1f4059a48d'],
+    }),
+]
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'],
+}
+
+moduleclass = 'data'