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# Copyright 2013-2021 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)
import os.path
from spack import *
class Cromwell(Package):
"""Cromwell is a Workflow Management System geared towards scientific
workflows.
"""
homepage = "http://cromwell.readthedocs.io/"
url = "https://github.com/broadinstitute/cromwell/releases/download/44/cromwell-44.jar"
version('44', sha256='8b411673f6b3c835c6031db3094a7404b9a371133794046fd295719d61e56db0', expand=False)
depends_on('java@8', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'cromwell-{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__), "cromwell.sh")
script = prefix.bin.cromwell
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('cromwell.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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