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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 Trimmomatic(Package):
"""A flexible read trimming tool for Illumina NGS data."""
homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
url = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
license("GPL-3.0-only")
# Older version aren't explicitly made available, but the URL
# works as we'd like it to, so...
version("0.39", sha256="2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca")
version("0.38", sha256="d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c")
version("0.36", sha256="4846c42347b663b9d6d3a8cef30da2aec89fc718bf291392c58e5afcea9f70fe")
version("0.33", sha256="6968583a6c5854a44fff7d427e7ccdcb8dc17f4616082dd390a0633f87a09e3d")
depends_on("java@8", type="run", when="@:0.38")
depends_on("java@8:", type="run", when="@0.39:")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "trimmomatic-{v}.jar".format(v=self.version.dotted)
install(jar_file, prefix.bin)
# Put the adapter files someplace sensible
install_tree("adapters", prefix.share.adapters)
# 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__), "trimmomatic.sh")
script = prefix.bin.trimmomatic
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("trimmomatic.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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