gatk package: new versions, updated helper script (#10459)
Closes #10168 * Add versions 4.1.0.0 and 4.0.12.0 * Replace md5 checksums with sha256 * Logic to generate a helper script for versions earlier than 4 was not running. This corrects the branch which controls whether this script is generated. * Constrain Java dependency to version 8 (GATK does not work with Java 11) * Avoid adding scripts that have dependencies not handled by Spack such as gcloud and google-chrome. These scripts are good candidates for later extensions.
This commit is contained in:
zschulte
Peter Scheibel
parent
cf754245fd
commit
a701c412bc
1 changed files with 72 additions and 40 deletions
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@ -3,59 +3,91 @@
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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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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"""Genome Analysis Toolkit
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Variant Discovery in High-Throughput Sequencing Data
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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/4.0.4.0/gatk-4.0.4.0.zip"
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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('4.0.11.0', sha256='5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536')
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version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
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url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
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version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
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url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
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version('3.8-1', 'a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c', 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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version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
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url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
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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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"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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"0581308d2a25f10d11d3dfd0d6e4d28e",
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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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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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# Install all executable non-script files to prefix bin
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jar_file = 'GenomeAnalysisTK.jar'
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install(jar_file, 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 settings
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if spec.satisfies('@:4.0'):
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return
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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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# 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('GenomeAnalysisTK.jar', join_path(prefix.bin,
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'GenomeAnalysisTK.jar'),
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script, **kwargs)
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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_environment(self, spack_env, run_env):
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run_env.prepend_path('GATK',
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join_path(self.prefix, 'bin',
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'GenomeAnalysisTK.jar'))
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run_env.prepend_path(
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"GATK", join_path(self.prefix, "bin", "GenomeAnalysisTK.jar")
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)
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