Commit ba4fea0f authored by Lukáš Krupčík's avatar Lukáš Krupčík

new file: b/BCFtools/BCFtools-1.8-intel-2017a.eb

	new file:   h/HTSlib/HTSlib-1.8-intel-2017a.eb
	new file:   s/SAMtools/SAMtools-1.8-intel-2017a.eb
parent 06ff1a30
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'
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'
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'
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