646771300d
* pushing partially done recipe for fast-gbs and platypus * modify platypus * change header * fast-gbs: change dependency type. * modify dependency type. * modify dependency type. * fast-gbs: Change dependency type to run.
55 lines
2.3 KiB
Python
55 lines
2.3 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 FastGbs(Package):
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"""A bioinformatic pipeline designed to extract a high-quality SNP catalog
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starting from FASTQ files obtained from sequencing
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genotyping-by-sequencing (GBS) libraries."""
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homepage = "https://bitbucket.org/jerlar73/fast-gbs"
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url = "https://bitbucket.org/jerlar73/fast-gbs"
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version('2017-01-25', git='https://bitbucket.org/jerlar73/fast-gbs.git', commit='3b3cbffa84d269419692067c6a3de08b3b88849c')
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depends_on('parallel', type='run')
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depends_on('python@2.7:', type='run')
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depends_on('sabre', type='run')
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depends_on('py-cutadapt', type='run')
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depends_on('bwa', type='run')
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depends_on('samtools', type='run')
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depends_on('platypus', type='run')
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depends_on('py-pyvcf', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('fastgbs.sh', prefix.bin)
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install('parameters.txt', prefix.bin)
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install('makeDir.sh', prefix.bin)
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install('makeBarcodeSabre.py', prefix.bin)
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install('vcf2txt.py', prefix.bin)
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install('txt2unix.sh', prefix.bin)
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