6a26322eb3
Most of these are perl packages that need to point to the meta docs site, and then a fair amount of http addresses that need to be https, and then the rest are usually documentation sites that no longer exist or were otherwise changes Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
142 lines
4.9 KiB
Python
142 lines
4.9 KiB
Python
# Copyright 2013-2021 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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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://gatk.broadinstitute.org/hc/en-us"
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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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"4.1.8.1",
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sha256="42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc",
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)
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version(
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"4.1.8.0",
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sha256="3ce1c2a15c44d0cfc9b2c26111f4518c215a5f9314072b4eb61f07ab5d01eef6",
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)
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version(
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"4.1.7.0",
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sha256="1ed6f7c3194563a16c53b66e64d1b16d3f5e919d057d9e60f0ae6570eb0882e3",
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)
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version(
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"4.1.6.0",
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sha256="1a8a0256693c0e1fb83d87b6da4bad4a182bfc2a762394650b627a882694c306",
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)
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version(
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"4.1.5.0",
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sha256="6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b",
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)
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version(
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"4.1.4.1",
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sha256="21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea",
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)
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version(
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"4.1.4.0",
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sha256="ae54a2b938f704e15ea03d1822b4ce80d9a02108dc3a2b482d80b93edae3d492",
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)
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version(
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"4.1.3.0",
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sha256="56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a",
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)
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version(
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"4.1.2.0",
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sha256="ffc5f9b3d4b35772ee5dac3060b59dc657f30e830745160671d84d732c30dc65",
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)
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version(
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"4.1.1.0",
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sha256="0d997aaf5c633643c07f0e5f74d0e20364a0f1304b04355bc6e073c65fab6554",
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)
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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://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2",
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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.bz2",
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url="https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2"
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)
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# Make r a variant. According to the gatk docs it is not essential and not
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# tested.
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# https://github.com/broadinstitute/gatk#R
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# Using R to generate plots
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# Certain GATK tools may optionally generate plots using the R installation
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# provided within the conda environment. If you are uninterested in plotting,
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# R is still required by several of the unit tests. Plotting is currently
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# untested and should be viewed as a convenience rather than a primary
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# output.
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variant('r', default=False, description='Use R for plotting')
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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: +r")
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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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install("*.jar", 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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