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# Copyright 2013-2023 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 RnaSeqc(Package):
"""RNA-SeQC is a java program which computes a series of quality control
metrics for RNA-seq data."""
homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
version(
"1.1.8",
sha256="0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793",
expand=False,
)
version(
"1.1.7",
sha256="78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3",
expand=False,
)
version(
"1.1.6",
sha256="76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6",
expand=False,
)
version(
"1.1.5",
sha256="1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9",
expand=False,
)
version(
"1.1.4",
sha256="eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6",
expand=False,
)
depends_on("java@8:", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "RNA-SeQC_v{0}.jar".format(self.version.dotted)
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__), "rna-seqc.sh")
script = join_path(prefix.bin, "rna-seqc")
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("RNA-SeQC_v{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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