diff --git a/b/BWA/BWA-0.7.17-intel-2020b.eb b/b/BWA/BWA-0.7.17-intel-2020b.eb new file mode 100644 index 00000000..95e6043a --- /dev/null +++ b/b/BWA/BWA-0.7.17-intel-2020b.eb @@ -0,0 +1,20 @@ +# IT4Innovations +# LK 2021 + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +dependencies = [('zlib', '1.2.11')] + +moduleclass = 'bio' diff --git a/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb b/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb new file mode 100644 index 00000000..16f11ded --- /dev/null +++ b/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb @@ -0,0 +1,38 @@ +# IT4Innovations +# LK 2021 + +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.0' +versionsuffix = '-Java-%(javaver)s-Python-%(pyver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio'