diff --git a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb index 20ce4bdd8d2..2aadd350563 100644 --- a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb @@ -21,6 +21,7 @@ dependencies = [ ('Velvet', '1.2.10', '-mt-kmer_191'), ('Exonerate', '2.4.0'), ('Pysam', '0.15.3'), + ('PyVCF', '0.6.8'), ] download_dep_fail = True @@ -33,6 +34,11 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + "evaluator.py --help", # requires PyVCF + "postprocess.py --help", +] + sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb new file mode 100644 index 00000000000..c7761dfa305 --- /dev/null +++ b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PyVCF' +version = '0.6.8' + +homepage = 'https://github.com/jamescasbon/PyVCF' +description = "A Variant Call Format reader for Python." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +dependencies = [('Pysam', '0.15.3')] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'vcf'} + +sanity_check_paths = { + 'files': ['bin/vcf_filter.py', 'bin/vcf_melt', 'bin/vcf_sample_filter.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "vcf_filter.py --help", + "vcf_sample_filter.py --help" +] + +sanity_pip_check = True + +moduleclass = 'bio'