43 lines
1.5 KiB
Python
43 lines
1.5 KiB
Python
# Copyright 2013-2019 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.path
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class Snpeff(Package):
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"""SnpEff is a variant annotation and effect prediction tool. It
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annotates and predicts the effects of genetic variants (such as
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amino acid changes)."""
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homepage = "http://snpeff.sourceforge.net/"
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url = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
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version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
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depends_on('jdk', type=('build', 'run'))
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def install(self, spec, prefix):
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install_tree('snpEff', prefix.bin)
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# Set up a helper script to call java on the jar files,
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# explicitly codes the path for java and the jar files.
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scripts = ['snpEff', 'SnpSift']
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for script in scripts:
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script_sh = join_path(os.path.dirname(__file__), script + ".sh")
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script_path = join_path(prefix.bin, script)
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install(script_sh, script_path)
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set_executable(script_path)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = self.spec['java'].prefix.bin.java
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kwargs = {'backup': False}
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filter_file('^java', java, script_path, **kwargs)
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filter_file(script + '.jar',
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join_path(prefix.bin, script + '.jar'),
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script_path, **kwargs)
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