bismark: Create new package (#7795)
* bismark: Create new package * bismark: fix dependency types
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var/spack/repos/builtin/packages/bismark/package.py
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var/spack/repos/builtin/packages/bismark/package.py
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##############################################################################
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# Copyright (c) 2013-2017, 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 Bismark(Package):
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"""A tool to map bisulfite converted sequence reads and determine cytosine
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methylation states"""
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homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
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url = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz"
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version('0.19.0', 'f403654aded77bf0d1dac1203867ded1')
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version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8')
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depends_on('bowtie2', type='run')
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depends_on('perl', type='run')
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depends_on('samtools', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('bam2nuc', prefix.bin)
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install('bismark', prefix.bin)
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install('bismark_genome_preparation', prefix.bin)
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install('bismark_methylation_extractor', prefix.bin)
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install('bismark2bedGraph', prefix.bin)
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install('bismark2report', prefix.bin)
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install('bismark2summary', prefix.bin)
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install('coverage2cytosine', prefix.bin)
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install('deduplicate_bismark', prefix.bin)
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install('filter_non_conversion', prefix.bin)
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install('NOMe_filtering', prefix.bin)
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