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# Copyright 2013-2020 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 CromwellWomtool(Package):
"""Command line utilities for interacting with the
Workflow Object Model (WOM).
"""
homepage = "https://cromwell.readthedocs.io/en/stable/WOMtool/"
url = "https://github.com/broadinstitute/cromwell/releases/download/44/womtool-44.jar"
version('44', sha256='b17c0f4933d7b136c7d9760f7858f6439e3c6371f12492e2aeaab3209c28f80a', expand=False)
depends_on('java@8', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'womtool-{0}.jar'.format(self.version)
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__), "womtool.sh")
script = prefix.bin.womtool
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('womtool.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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