Commit 552506bd authored by Lukáš Krupčík's avatar Lukáš Krupčík

new file: b/BCFtools/BCFtools-1.9-intel-2017a.eb

	new file:   h/HTSlib/HTSlib-1.9-intel-2017a.eb
	modified:   o/OpenFOAM/OpenFOAM-6-foss-2018a.eb
	new file:   r/R/MCMCpack-1.4-4_icpc-wd308.patch
	modified:   r/R/R-3.5.3-intel-2017a.eb
	modified:   s/SAMtools/SAMtools-1.9-intel-2017a.eb
parent 0380dc11
Pipeline #7632 failed with stage
in 21 seconds
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'BCFtools'
version = '1.9'
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']
dependencies = [
('zlib', '1.2.11', '', True),
('HTSlib', '1.9'),
('GSL', '2.5'),
('XZ', '5.2.4', '', 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'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'HTSlib'
version = '1.9'
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),
('bzip2', '1.0.6', '', True),
('XZ', '5.2.4', '', True),
]
sanity_check_paths = {
'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT],
'dirs': [],
}
moduleclass = 'bio'
......@@ -38,4 +38,6 @@ builddependencies = [
('flex', '2.6.4', '', True),
]
modextrapaths = {'PATH': 'OpenFOAM-%(version)s/bin'}
moduleclass = 'cae'
--- MCMCpack/src/Makevars.in.orig 2019-04-24 08:41:09.117144775 +0200
+++ MCMCpack/src/Makevars.in 2019-04-24 08:41:51.556233445 +0200
@@ -1,2 +1,2 @@
-PKG_CPPFLAGS = -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC @MV_HAVE_IEEEFP_H@ @MV_HAVE_TRUNC@
-
+PKG_CPPFLAGS = -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC @MV_HAVE_IEEEFP_H@ @MV_HAVE_TRUNC@
+PKG_CXXFLAGS = -wd308
......@@ -65,6 +65,7 @@ exts_default_options = {
'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive
'http://cran.r-project.org/src/contrib/', # current version of packages
'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages
'https://bioconductor.org/packages/release/bioc/src/contrib/',
],
'source_tmpl': '%(name)s_%(version)s.tar.gz',
}
......@@ -2059,6 +2060,7 @@ exts_list = [
}),
('MCMCpack', '1.4-4', {
'checksums': ['97e193d628f7161e59288ed594a313af3a520bf30d5a95f1ede0cb2a567cf9f7'],
'patches' : [('MCMCpack-1.4-4_icpc-wd308.patch')],
}),
('shinythemes', '1.1.2', {
'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'],
......@@ -2070,6 +2072,7 @@ exts_list = [
'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'],
}),
# qualimap dependencies
('BiocGenerics', '0.28.0'),
('Biobase', '2.42.0'),
('NOISeq', '2.26.1'),
]
......
......@@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2]
dependencies = [
('ncurses', '6.0', '', True),
('zlib', '1.2.11', '', True),
('XZ', '5.2.3', '', True),
('XZ', '5.2.4', '', True),
('bzip2', '1.0.6', '', True),
]
......
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