eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
41 lines
1.5 KiB
Python
41 lines
1.5 KiB
Python
# Copyright 2013-2018 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 Pilon(Package):
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"""Pilon is an automated genome assembly improvement and variant
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detection tool."""
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homepage = "https://github.com/broadinstitute/pilon"
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url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
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version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
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version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
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depends_on('java@1.7:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'pilon-{0}.jar'.format(self.version.dotted)
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install(jar_file, prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "pilon.sh")
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script = prefix.bin.pilon
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install(script_sh, script)
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set_executable(script)
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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 = {'ignore_absent': False, 'backup': False, 'string': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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