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
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class Genomefinisher(Package):
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"""GFinisher is an application tools for refinement and finalization of
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prokaryotic genomes assemblies using the bias of GC Skew to identify
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assembly errors and organizes the contigs/scaffolds with genomes
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references."""
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homepage = "http://gfinisher.sourceforge.net"
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url = "https://sourceforge.net/projects/gfinisher/files/GenomeFinisher_1.4.zip"
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version('1.4', 'bd9bbca656fe15ecbe615c4732714bc7')
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depends_on('java@8:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'GenomeFinisher.jar'
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install(jar_file, prefix.bin)
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install_tree('lib', prefix.lib)
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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__), "genomefinisher.sh")
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script = prefix.bin.genomefinisher
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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 jar file
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# jar file.
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java = 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(jar_file, join_path(prefix.bin, jar_file),
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script, **kwargs)
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