diff --git a/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..1bcf3419c63 --- /dev/null +++ b/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'OptiType' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/FRED-2/OptiType' +description = """ OptiType is a novel HLA genotyping algorithm based on integer linear programming, + capable of producing accurate 4-digit HLA genotyping predictions from NGS data + by simultaneously selecting all major and minor HLA Class I alleles. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FRED-2/OptiType/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7cc74b3a163afcd9f734c56b6753781d7ffe56b8f92874b788088147cf62cd6a'] + +dependencies = [ + ('future', '0.16.0', versionsuffix), + ('GLPK', '4.65'), + ('HDF5', '1.10.2'), + ('matplotlib', '2.2.3', versionsuffix), + ('Python', '2.7.15'), + ('Pyomo', '5.5.0', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('PyTables', '3.4.4', versionsuffix), + ('SAMtools', '1.9'), + ('SeqAn', '2.4.0'), +] + +postinstallcmds = [ + 'cp %(installdir)s/config.ini{.example,}', + 'sed -i -e "s|/path/to/razers3|$EBROOTSEQAN/bin/razers3|" %(installdir)s/config.ini', + 'sed -i -e "1i #!/usr/bin/env python" %(installdir)s/OptiTypePipeline.py', +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['config.ini', 'hlatyper.py', 'model.py', 'OptiTypePipeline.py'], + 'dirs': [], +} + +sanity_check_commands = [( + 'OptiTypePipeline.py -i %(installdir)s/test/exome/NA11995_SRR766010_1_fished.fastq ' + '%(installdir)s/test/exome/NA11995_SRR766010_2_fished.fastq --dna -v -o %(builddir)s/' +)] + +moduleclass = 'bio'