41 lines
1.4 KiB
Python
41 lines
1.4 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 Varscan(Package):
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"""Variant calling and somatic mutation/CNV detection for next-generation
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sequencing data"""
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homepage = "http://dkoboldt.github.io/varscan/"
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url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
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version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False)
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depends_on('java', type=('build', 'run'))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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mkdirp(prefix.jar)
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jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted)
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install(jar_file, prefix.jar)
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script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
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script = prefix.bin.varscan
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install(script_sh, script)
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set_executable(script)
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java = join_path(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('varscan.jar', join_path(prefix.jar, jar_file),
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script, **kwargs)
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def setup_environment(self, spack_env, run_env):
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run_env.set('VARSCAN_HOME', self.prefix.jar)
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run_env.set('CLASSPATH', self.prefix.jar)
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