diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.5.7-gompi-2023b.eb new file mode 100644 index 00000000000..08fdaab9f31 --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7c564210edb --- /dev/null +++ b/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' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0210-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9e8ac11247f --- /dev/null +++ b/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'