39 lines
1.4 KiB
Python
39 lines
1.4 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 os
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class Orthofiller(Package):
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"""OrthoFiller: Identifying missing annotations for evolutionarily
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conserved genes."""
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homepage = "https://github.com/mpdunne/orthofiller/"
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url = "https://github.com/mpdunne/orthofiller/archive/1.1.4.tar.gz"
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version('1.1.4', sha256='a693a3372a3f05041ce30cbf84da1be88e85eae4effe32dbd7809ccef119a295')
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depends_on('augustus', type='run')
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depends_on('bedtools2@2.25.0', type='run')
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depends_on('hmmer', type='run')
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depends_on('orthofinder', type='run')
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depends_on('python@2.7:', type='run')
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depends_on('py-biopython', type='run')
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depends_on('py-scipy', type='run')
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depends_on('r', type='run')
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depends_on('r-gamlss', type='run')
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depends_on('mafft', type='run')
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def install(self, spec, prefix):
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# orthofiller tests for common unix programs using man
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# runtime modules will quickly overflow the maximum MANPATH;
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# we change the man tests to use which instead, more reliable anyway
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filter_file('"man "', '"which "', 'OrthoFiller.py', string=True)
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os.chmod('OrthoFiller.py', 0o755)
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mkdirp(prefix.bin)
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install('OrthoFiller.py', prefix.bin)
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