60 lines
2.4 KiB
Python
60 lines
2.4 KiB
Python
##############################################################################
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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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import glob
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import os
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class Hybpiper(Package):
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"""HybPiper was designed for targeted sequence capture, in which DNA
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sequencing libraries are enriched for gene regions of interest,
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especially for phylogenetics. HybPiper is a suite of Python scripts
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that wrap and connect bioinformatics tools in order to extract target
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sequences from high-throughput DNA sequencing reads"""
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homepage = "https://github.com/mossmatters/HybPiper"
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url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
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version('1.2.0', '0ad78e9ca5e3f23ae0eb6236b07e1780')
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depends_on('python@2.7:', type=('build', 'run'))
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depends_on('py-biopython', type=('build', 'run'))
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depends_on('exonerate')
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depends_on('blast-plus')
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depends_on('spades')
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depends_on('parallel')
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depends_on('bwa')
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depends_on('samtools')
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def setup_envionment(self, spack_env, run_env):
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run_env.set('HYBPIPER_HOME', prefix)
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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files = glob.iglob("*.py")
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for file in files:
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if os.path.isfile(file):
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install(file, prefix.bin)
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