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| -rwxr-xr-x | var/spack/repos/builtin/packages/gatk/gatk.sh | 4 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/gatk/package.py | 87 |
2 files changed, 91 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/gatk/gatk.sh b/var/spack/repos/builtin/packages/gatk/gatk.sh new file mode 100755 index 0000000000..2bd68247a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/gatk/gatk.sh @@ -0,0 +1,4 @@ +#!/bin/sh +# convenience wrapper for the gatk jar file +java -jar GenomeAnalysisTK.jar "$@" + diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py new file mode 100644 index 0000000000..728fae94da --- /dev/null +++ b/var/spack/repos/builtin/packages/gatk/package.py @@ -0,0 +1,87 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/spack/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +# +# This is a template package file for Spack. We've put "FIXME" +# next to all the things you'll want to change. Once you've handled +# them, you can save this file and test your package like this: +# +# spack install gatk +# +# You can edit this file again by typing: +# +# spack edit gatk +# +# See the Spack documentation for more information on packaging. +# If you submit this package back to Spack as a pull request, +# please first remove this boilerplate and all FIXME comments. +# +from spack import * +from shutil import copyfile +import glob +import os.path +import re + + +class Gatk(Package): + """Genome Analysis Toolkit + Variant Discovery in High-Throughput Sequencing Data + """ + homepage = "http://broadinstitute.github.io/gatk/" + url = "https://software.broadinstitute.org/gatk/download/auth?package=GATK" + _urlfmt = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz" + + version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz', + url="https://software.broadinstitute.org/gatk/download/auth?package=GATK") + + depends_on('java@8:', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + # The list of files to install varies with release... + # ... but skip the spack-{build.env}.out files. + files = [x for x in glob.glob("*") if not re.match("^spack-", x)] + for f in files: + install(f, prefix.bin) + + # 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") + copyfile(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')) |