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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os.path
class Varscan(Package):
"""Variant calling and somatic mutation/CNV detection for next-generation
sequencing data"""
homepage = "http://dkoboldt.github.io/varscan/"
url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False)
depends_on('java', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.jar)
jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted)
install(jar_file, prefix.jar)
script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
script = prefix.bin.varscan
install(script_sh, script)
set_executable(script)
java = join_path(self.spec['java'].prefix, 'bin', 'java')
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('varscan.jar', join_path(prefix.jar, jar_file),
script, **kwargs)
def setup_environment(self, spack_env, run_env):
run_env.set('VARSCAN_HOME', self.prefix)
run_env.set('CLASSPATH', self.prefix.jar)
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