45 lines
1.5 KiB
Python
45 lines
1.5 KiB
Python
# Copyright 2013-2023 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 Varscan(Package):
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"""Variant calling and somatic mutation/CNV detection for next-generation
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sequencing data"""
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homepage = "https://dkoboldt.github.io/varscan/"
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url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
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version(
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"2.4.2",
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sha256="34ff6462f91fb6ed3f11e867ab4a179efae5dd8214b97fa261fc616f23d4d031",
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expand=False,
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)
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depends_on("java", type=("build", "run"))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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mkdirp(prefix.jar)
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jar_file = "VarScan.v{v}.jar".format(v=self.version.dotted)
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install(jar_file, prefix.jar)
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script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
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script = prefix.bin.varscan
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install(script_sh, script)
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set_executable(script)
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java = join_path(self.spec["java"].prefix, "bin", "java")
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kwargs = {"ignore_absent": False, "backup": False, "string": False}
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filter_file("^java", java, script, **kwargs)
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filter_file("varscan.jar", join_path(prefix.jar, jar_file), script, **kwargs)
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def setup_run_environment(self, env):
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env.set("VARSCAN_HOME", self.prefix.jar)
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env.set("CLASSPATH", self.prefix.jar)
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