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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
from spack.package import *
class Chexmix(Package):
"""ChExMix: the ChIP-exo mixture model. ChExMix aims to characterize protein-DNA binding
subtypes in ChIP-exo experiments."""
homepage = "http://mahonylab.org/software/chexmix"
url = "https://github.com/seqcode/chexmix/releases/download/v0.51/chexmix.v0.51.jar"
# The naming of the .jar files is inconsistent on GitHub. Until this is resolved, downloads
# that don't match the above url spec will need to be renamed - see rename_versions().
version(
"0.52",
url="https://github.com/seqcode/chexmix/releases/download/v0.52/chexmix.v0.52.public.jar",
sha256="7f856921b6071092cfcf226e4f99d9ab80587cf05502b41d00b8e5e16ccbfcdd",
expand=False,
)
depends_on("java@8:", type="run")
depends_on("meme", type="run")
@run_before("install")
def rename_versions(self):
if self.version == Version("0.52"):
os.rename("chexmix.v0.52.public.jar", "chexmix.v0.52.jar")
def install(self, spec, prefix):
# install .jar file
mkdirp(prefix.bin)
jar_file = "chexmix.v{0}.jar".format(self.version)
install(jar_file, prefix.bin)
# create a helper script to launch the .jar
script_sh = join_path(os.path.dirname(__file__), "chexmix.sh")
script = prefix.bin.chexmix
install(script_sh, script)
set_executable(script)
# set 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("chexmix.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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