94 lines
3.2 KiB
Python
94 lines
3.2 KiB
Python
# Copyright 2013-2019 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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import glob
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from spack import *
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class Gatk(Package):
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"""
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Genome Analysis Toolkit
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Variant Discovery in High-Throughput Sequencing Data
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"""
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homepage = "https://software.broadinstitute.org/gatk/"
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url = "https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip"
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list_url = "https://github.com/broadinstitute/gatk/releases"
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version(
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"4.1.0.0",
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sha256="148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d",
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)
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version(
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"4.0.12.0",
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sha256="733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f",
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)
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version(
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"4.0.11.0",
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sha256="5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536",
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)
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version(
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"4.0.8.1",
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sha256="e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9",
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)
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version(
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"4.0.4.0",
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sha256="801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4",
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)
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version(
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"3.8-1",
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sha256="a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c",
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extension="tar.bz2",
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url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef",
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)
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version(
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"3.8-0",
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sha256="d1017b851f0cc6442b75ac88dd438e58203fa3ef1d1c38eb280071ae3803b9f1",
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extension="tar.gz",
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url="https://software.broadinstitute.org/gatk/download/auth?package=GATK",
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)
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depends_on("java@8", type="run")
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depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:")
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depends_on("r@3.2:", type="run", when="@4.0:")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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# For ver 3.x will install "GenomeAnalysisTK.jar"
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# For ver 4.x will install both "gatk-package-<ver>-local.jar"
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# and "gatk-package-<ver>-spark.jar"
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for file in glob.glob("*.jar"):
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install(file, prefix.bin)
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# Skip helper script for versions >4.0
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if spec.satisfies("@4.0:"):
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install("gatk", prefix.bin)
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else:
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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__), "gatk.sh")
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script = join_path(prefix.bin, "gatk")
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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 = 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(
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"GenomeAnalysisTK.jar",
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join_path(prefix.bin, "GenomeAnalysisTK.jar"),
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script,
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**kwargs
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)
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def setup_run_environment(self, env):
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env.prepend_path(
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"GATK", join_path(self.prefix.bin, "GenomeAnalysisTK.jar")
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)
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