51 lines
1.9 KiB
Python
51 lines
1.9 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os.path
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from spack.package import *
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class Qorts(RPackage):
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"""The QoRTs software package is a fast, efficient, and portable
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multifunction toolkit designed to assist in the analysis, quality
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control, and data management of RNA-Seq and DNA-Seq datasets. Its
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primary function is to aid in the detection and identification of
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errors, biases, and artifacts produced by high-throughput sequencing
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technology."""
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homepage = "https://github.com/hartleys/QoRTs"
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urls = ["https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"]
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version("1.2.42", sha256="c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08")
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depends_on("java", type="run")
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resource(
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name="QoRTs.jar",
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url="https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar",
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sha256="e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce",
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placement="jarfile",
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expand=False,
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)
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@run_after("install")
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def install_jar(self):
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install_tree(join_path(self.stage.source_path, "jarfile"), self.prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
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script = self.prefix.bin.QoRTs
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install(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = self.spec["java"].prefix.bin.java
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kwargs = {"backup": False}
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filter_file("^java", java, script, **kwargs)
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filter_file("QoRTs.jar", join_path(self.prefix.bin, "QoRTs.jar"), script, **kwargs)
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