diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/varscan/package.py | 59 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/varscan/varscan.sh | 3 |
2 files changed, 62 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/varscan/package.py b/var/spack/repos/builtin/packages/varscan/package.py new file mode 100644 index 0000000000..f4c2ae029d --- /dev/null +++ b/var/spack/repos/builtin/packages/varscan/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013-2016, 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/llnl/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 +############################################################################## +from spack import * +import os.path + + +class Varscan(Package): + """Variant calling and somatic mutation/CNV detection for next-generation + sequencing data""" + + homepage = "http://dkoboldt.github.io/varscan/" + url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar" + + version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False) + + depends_on('java', type=('build', 'run')) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + mkdirp(prefix.jar) + jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted) + install(jar_file, prefix.jar) + + script_sh = join_path(os.path.dirname(__file__), "varscan.sh") + script = prefix.bin.varscan + install(script_sh, script) + set_executable(script) + + 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('varscan.jar', join_path(prefix.jar, jar_file), + script, **kwargs) + + def setup_environment(self, spack_env, run_env): + run_env.set('VARSCAN_HOME', self.prefix) + run_env.set('CLASSPATH', self.prefix.jar) diff --git a/var/spack/repos/builtin/packages/varscan/varscan.sh b/var/spack/repos/builtin/packages/varscan/varscan.sh new file mode 100644 index 0000000000..71824a46c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/varscan/varscan.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the astral jar file +java $JAVA_ARGS $JAVA_OPTS -jar varscan.jar "$@" |