8cbd349cb4
Some packages had incorrect checksums because they needed to be downloaded from a new place or the package needed tweaking somehow. These packages to sha256 and the new checksums have been verified by fetching over https.
43 lines
1.6 KiB
Python
43 lines
1.6 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://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
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version('2017-11-24', sha256='d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244')
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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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