43 lines
1.5 KiB
Python
43 lines
1.5 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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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git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
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version('1.3.1', sha256='7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf')
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version('1.2.0', sha256='34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57')
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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_run_environment(self, env):
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env.set('HYBPIPER_HOME', self.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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