diff --git a/b/BCFtools/BCFtools-1.8-intel-2017a.eb b/b/BCFtools/BCFtools-1.8-intel-2017a.eb new file mode 100644 index 00000000..25d7f679 --- /dev/null +++ b/b/BCFtools/BCFtools-1.8-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.8' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +#patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('HTSlib', '1.8'), + ('GSL', '2.3'), + ('XZ', '5.2.3', '', True), +] + +parallel = 1 + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/h/HTSlib/HTSlib-1.8-intel-2017a.eb b/h/HTSlib/HTSlib-1.8-intel-2017a.eb new file mode 100644 index 00000000..4a3046d0 --- /dev/null +++ b/h/HTSlib/HTSlib-1.8-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.8' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('XZ', '5.2.3', '', True), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/s/SAMtools/SAMtools-1.8-intel-2017a.eb b/s/SAMtools/SAMtools-1.8-intel-2017a.eb new file mode 100644 index 00000000..0dbca6c1 --- /dev/null +++ b/s/SAMtools/SAMtools-1.8-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'SAMtools' +version = '1.8' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +#patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0', '', True), + ('zlib', '1.2.11', '', True), + ('XZ', '5.2.3', '', True), +] + +moduleclass = 'bio'