75 lines
3.3 KiB
Python
75 lines
3.3 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Vcftools(AutotoolsPackage):
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"""VCFtools is a program package designed for working with VCF files,
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such as those generated by the 1000 Genomes Project. The aim of
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VCFtools is to provide easily accessible methods for working
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with complex genetic variation data in the form of VCF files.
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"""
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homepage = "https://vcftools.github.io/"
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url = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"
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# this is "a pre-release"
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# version('0.1.15', '61045197848dea20a0158d2faf02e5be')
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version('0.1.14', 'a110662535651caa6cc8c876216a9f77')
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depends_on('perl', type=('build', 'run'))
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depends_on('zlib')
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# this needs to be in sync with what setup_environment adds to
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# PERL5LIB below
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def configure_args(self):
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return ['--with-pmdir={0}'.format(self.prefix.lib)]
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@run_before('install')
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def filter_sbang(self):
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"""Run before install so that the standard Spack sbang install hook
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can fix up the path to the perl binary.
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"""
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with working_dir('src/perl'):
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match = '^#!/usr/bin/env perl'
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substitute = "#!{perl}".format(perl=self.spec['perl'].command.path)
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# tab-to-vcf added in 0.1.15
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files = ['fill-aa', 'fill-an-ac', 'fill-fs',
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'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
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'vcf-compare', 'vcf-concat', 'vcf-consensus',
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'vcf-contrast', 'vcf-convert',
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'vcf-fix-newlines', 'vcf-fix-ploidy',
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'vcf-indel-stats', 'vcf-isec', 'vcf-merge',
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'vcf-phased-join', 'vcf-query',
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'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats',
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'vcf-subset', 'vcf-to-tab', 'vcf-tstv',
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'vcf-validator', ]
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kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
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filter_file(match, substitute, *files, **kwargs)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PERL5LIB', self.prefix.lib)
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