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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 Qorts(RPackage):
"""The QoRTs software package is a fast, efficient, and portable
multifunction toolkit designed to assist in the analysis, quality
control, and data management of RNA-Seq and DNA-Seq datasets. Its
primary function is to aid in the detection and identification of
errors, biases, and artifacts produced by high-throughput sequencing
technology."""
homepage = "https://github.com/hartleys/QoRTs"
url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
version("1.2.42", sha256="c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08")
depends_on("java", type="run")
resource(
name="QoRTs.jar",
url="https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar",
sha256="e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce",
placement="jarfile",
expand=False,
)
@run_after("install")
def install_jar(self):
install_tree(join_path(self.stage.source_path, "jarfile"), self.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__), "QoRTs.sh")
script = self.prefix.bin.QoRTs
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 = {"backup": False}
filter_file("^java", java, script, **kwargs)
filter_file("QoRTs.jar", join_path(self.prefix.bin, "QoRTs.jar"), script, **kwargs)
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