ComputeVM: VCFtools-0.1.12b-goolf-1.7.20-Perl-5.20.2-bare.eb

# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild

easyblock = 'MakeCp'

name = 'VCFtools'
namelower = name.lower()
version = '0.1.12b'

homepage = "http://vcftools.sourceforge.net/"
description = """The aim of VCFtools is to provide 
 methods for working with VCF files: validating, 
 merging, comparing and calculate some basic population
 genetic statistics. """

toolchain = {'name': 'goolf', 'version': '1.7.20'}

#
# Example URL:
# http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.12b.tar.gz?ts=1429189285&use_mirror=autoselect
#
import time
seconds_after_epoch = int(time.time())
source_urls = [('http://downloads.sourceforge.net/project/%s' % namelower, '?ts=%s&use_mirror=autoselect' % seconds_after_epoch)]
sources = ['%(namelower)s_%(version)s.tar.gz']

perl = 'Perl'
perlver = '5.20.2'
perlversuffix = '-bare'
versionsuffix = '-%s-%s%s' % (perl, perlver, perlversuffix)
dependencies = [
    (perl, perlver, perlversuffix),
    ('tabix', '0.2.6')
]

vcf_executables = ['fill-aa', 'fill-an-ac', 'fill-fs', 'fill-ref-md5', 
    'vcf-annotate', 'vcf-compare', 'vcf-concat', 'vcf-consensus', 'vcf-contrast', 
    'vcf-convert', 'vcf-fix-ploidy', 'vcf-indel-stats', 'vcf-isec', 'vcf-merge', 
    'vcf-phased-join', 'vcf-query', 'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats', 
    'vcf-subset', 'vcftools', 'vcf-to-tab', 'vcf-tstv', 'vcf-validator'
]

files_to_copy = ['bin', 'lib', 'examples', (['bin/man1'], 'man')]

modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'}

#
# Remove manual in wrong location.
#
postinstallcmds = ['rm -Rf %(installdir)s/bin/man1/']

#
# Check if all binaries from the suite are present.
#
sanity_check_paths = {
    'files': ['bin/%s' % x for x in vcf_executables],
    'dirs': [],
}

moduleclass = 'bio'