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# Copyright 2013-2024 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.package import *
class Cromwell(Package):
"""Cromwell is a Workflow Management System geared towards scientific
workflows"""
homepage = "https://cromwell.readthedocs.io/"
url = "https://github.com/broadinstitute/cromwell/releases/download/44/cromwell-44.jar"
version(
"85",
sha256="100f6c61df72b4079b3ad0f03e8f73e6e2c0afe99d212ec8d42faf4bd4de1e23",
expand=False,
)
version(
"44",
sha256="8b411673f6b3c835c6031db3094a7404b9a371133794046fd295719d61e56db0",
expand=False,
)
depends_on("java@11", when="@60:", type="run")
depends_on("java@8", when="@:59", 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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