diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb new file mode 100644 index 00000000000..0c101c27d2f --- /dev/null +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20240703-foss-2023a-Python-3.11.3.eb @@ -0,0 +1,64 @@ +easyblock = 'MakeCp' + +name = 'OPERA-MS' +local_commit = '026f9a5' +version = '0.9.0-20240703' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/CSB5/OPERA-MS' +description = """OPERA-MS is a hybrid metagenomic assembler which combines the + advantages of short and long-read technologies to provide high quality + assemblies, addressing issues of low contiguity for short-read only assemblies, + and low base-pair quality for long-read only assemblies.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['72a3e16287dd1f2098adac41930d6a54779a033f5bf78c2659580afae5a7280c'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('Statistics-R', '0.34'), + ('Python', '3.11.3'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + 'OPERA-MS.pl', + 'bin', + 'src_utils', + 'tools_opera_ms', + (['OPERA-LG/bin'], 'OPERA-LG'), +] + +postinstallcmds = [ + "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", + 'chmod +x %(installdir)s/bin/OPERA-MS', + 'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl', + '%(installdir)s/bin/OPERA-MS ' + ' '.join([ + '--contig-file test_files/contigs.fasta', + '--short-read1 test_files/R1.fastq.gz', + '--short-read2 test_files/R2.fastq.gz', + '--long-read test_files/long_read.fastq', + '--no-ref-clustering', + '--out-dir $TMPDIR', + ]), +] + +fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl'] +fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/OPERA-MS'], + 'dirs': [], +} + +sanity_check_commands = [ + 'OPERA-MS --help', + 'OPERA-MS check-dependency', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb new file mode 100644 index 00000000000..7a351d75a26 --- /dev/null +++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Statistics-R' +version = '0.34' + +homepage = 'https://metacpan.org/pod/Statistics::R' +description = "Perl interface with the R statistical program" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY'] +sources = [SOURCE_TAR_GZ] +checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('R', '4.3.2'), +] + +options = {'modulename': 'Statistics::R'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'], +} + +moduleclass = 'data'