178476d8c8
* add new package cromwell * fix flake8 errors, add cromwell-womtool package * change name of cromwell to cromwell-server * renamed cromwell-server to just cromwell * update description to what is in the project docs * fixing format call for python2.6 compatibility
41 lines
1.5 KiB
Python
41 lines
1.5 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 CromwellWomtool(Package):
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"""Command line utilities for interacting with the
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Workflow Object Model (WOM).
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"""
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homepage = "https://cromwell.readthedocs.io/en/stable/WOMtool/"
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url = "https://github.com/broadinstitute/cromwell/releases/download/44/womtool-44.jar"
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version('44', sha256='b17c0f4933d7b136c7d9760f7858f6439e3c6371f12492e2aeaab3209c28f80a', expand=False)
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depends_on('java@8', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'womtool-{0}.jar'.format(self.version)
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install(jar_file, prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "womtool.sh")
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script = prefix.bin.womtool
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install(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = 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('womtool.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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