| 1 | # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild |
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| 2 | |
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| 3 | easyblock = 'MakeCp' |
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| 4 | |
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| 5 | name = 'VCFtools' |
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| 6 | namelower = name.lower() |
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| 7 | version = '0.1.12b' |
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| 8 | |
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| 9 | homepage = "http://vcftools.sourceforge.net/" |
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| 10 | description = """The aim of VCFtools is to provide |
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| 11 | methods for working with VCF files: validating, |
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| 12 | merging, comparing and calculate some basic population |
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| 13 | genetic statistics. """ |
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| 14 | |
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| 15 | toolchain = {'name': 'goolf', 'version': '1.7.20'} |
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| 16 | |
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| 17 | # |
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| 18 | # Example URL: |
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| 19 | # http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.12b.tar.gz?ts=1429189285&use_mirror=autoselect |
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| 20 | # |
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| 21 | import time |
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| 22 | seconds_after_epoch = int(time.time()) |
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| 23 | source_urls = [('http://downloads.sourceforge.net/project/%s' % namelower, '?ts=%s&use_mirror=autoselect' % seconds_after_epoch)] |
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| 24 | sources = ['%(namelower)s_%(version)s.tar.gz'] |
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| 25 | |
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| 26 | perl = 'Perl' |
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| 27 | perlver = '5.20.2' |
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| 28 | perlversuffix = '-bare' |
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| 29 | versionsuffix = '-%s-%s%s' % (perl, perlver, perlversuffix) |
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| 30 | dependencies = [ |
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| 31 | (perl, perlver, perlversuffix), |
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| 32 | ('tabix', '0.2.6') |
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| 33 | ] |
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| 34 | |
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| 35 | vcf_executables = ['fill-aa', 'fill-an-ac', 'fill-fs', 'fill-ref-md5', |
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| 36 | 'vcf-annotate', 'vcf-compare', 'vcf-concat', 'vcf-consensus', 'vcf-contrast', |
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| 37 | 'vcf-convert', 'vcf-fix-ploidy', 'vcf-indel-stats', 'vcf-isec', 'vcf-merge', |
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| 38 | 'vcf-phased-join', 'vcf-query', 'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats', |
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| 39 | 'vcf-subset', 'vcftools', 'vcf-to-tab', 'vcf-tstv', 'vcf-validator' |
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| 40 | ] |
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| 41 | |
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| 42 | files_to_copy = ['bin', 'lib', 'examples', (['bin/man1'], 'man')] |
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| 43 | |
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| 44 | modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} |
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| 45 | |
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| 46 | # |
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| 47 | # Remove manual in wrong location. |
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| 48 | # |
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| 49 | postinstallcmds = ['rm -Rf %(installdir)s/bin/man1/'] |
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| 50 | |
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| 51 | # |
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| 52 | # Check if all binaries from the suite are present. |
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| 53 | # |
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| 54 | sanity_check_paths = { |
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| 55 | 'files': ['bin/%s' % x for x in vcf_executables], |
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| 56 | 'dirs': [], |
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| 57 | } |
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| 58 | |
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| 59 | moduleclass = 'bio' |
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