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# Copyright 2013-2019 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 Pilon(Package):
"""Pilon is an automated genome assembly improvement and variant
detection tool."""
homepage = "https://github.com/broadinstitute/pilon"
url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
depends_on('java@1.7:', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'pilon-{0}.jar'.format(self.version.dotted)
install(jar_file, prefix.bin)
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "pilon.sh")
script = prefix.bin.pilon
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = self.spec['java'].prefix.bin.java
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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