2017-08-29 04:25:19 +08:00
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##############################################################################
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2017-09-07 11:44:16 +08:00
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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2017-08-29 04:25:19 +08:00
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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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2017-11-05 08:08:04 +08:00
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# For details, see https://github.com/spack/spack
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2017-08-29 04:25:19 +08:00
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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 Redundans(Package):
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"""Redundans pipeline assists an assembly of heterozygous genomes."""
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homepage = "https://github.com/Gabaldonlab/redundans"
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url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
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version('0.13c', '2003fb7c70521f5e430553686fd1a594')
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depends_on('python', type=('build', 'run'))
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depends_on('py-pyscaf', type=('build', 'run'))
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depends_on('py-fastaindex', type=('build', 'run'))
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depends_on('perl', type=('build', 'run'))
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depends_on('sspace-standard')
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depends_on('bwa')
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depends_on('last')
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depends_on('gapcloser')
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depends_on('parallel')
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depends_on('snap-berkeley')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('redundans.py', prefix.bin)
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with working_dir('bin'):
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install('fasta2homozygous.py', prefix.bin)
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install('fasta2split.py', prefix.bin)
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install('fastq2insert_size.py', prefix.bin)
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install('fastq2mates.py', prefix.bin)
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install('fastq2shuffled.py', prefix.bin)
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install('fastq2sspace.py', prefix.bin)
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install('filterReads.py', prefix.bin)
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