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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os.path
import glob
from spack import *
class Gatk(Package):
"""
Genome Analysis Toolkit
Variant Discovery in High-Throughput Sequencing Data
"""
homepage = "https://software.broadinstitute.org/gatk/"
url = "https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip"
list_url = "https://github.com/broadinstitute/gatk/releases"
version(
"4.1.0.0",
sha256="148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d",
)
version(
"4.0.12.0",
sha256="733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f",
)
version(
"4.0.11.0",
sha256="5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536",
)
version(
"4.0.8.1",
sha256="e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9",
)
version(
"4.0.4.0",
sha256="801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4",
)
version(
"3.8-1",
"a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c",
extension="tar.bz2",
url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef",
)
version(
"3.8-0",
"0581308d2a25f10d11d3dfd0d6e4d28e",
extension="tar.gz",
url="https://software.broadinstitute.org/gatk/download/auth?package=GATK",
)
depends_on("java@8", type="run")
depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:")
depends_on("r@3.2:", type="run", when="@4.0:")
def install(self, spec, prefix):
mkdirp(prefix.bin)
# For ver 3.x will install "GenomeAnalysisTK.jar"
# For ver 4.x will install both "gatk-package-<ver>-local.jar"
# and "gatk-package-<ver>-spark.jar"
for file in glob.glob("*.jar"):
install(file, prefix.bin)
# Skip helper script for versions >4.0
if spec.satisfies("@4.0:"):
install("gatk", prefix.bin)
else:
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
script = join_path(prefix.bin, "gatk")
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = join_path(self.spec["java"].prefix, "bin", "java")
kwargs = {"ignore_absent": False, "backup": False, "string": False}
filter_file("^java", java, script, **kwargs)
filter_file(
"GenomeAnalysisTK.jar",
join_path(prefix.bin, "GenomeAnalysisTK.jar"),
script,
**kwargs
)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path(
"GATK", join_path(self.prefix, "bin", "GenomeAnalysisTK.jar")
)
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