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| -rw-r--r-- | var/spack/repos/builtin/packages/pgdspider/package.py | 57 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/pgdspider/pgdspider.sh | 3 |
2 files changed, 60 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py new file mode 100644 index 0000000000..60dfdc12f4 --- /dev/null +++ b/var/spack/repos/builtin/packages/pgdspider/package.py @@ -0,0 +1,57 @@ +############################################################################## +# 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 Pgdspider(Package): + """"PGDSpider is a powerful automated data conversion tool for population + genetic and genomics programs""" + + homepage = "http://www.cmpg.unibe.ch/software/PGDSpider" + url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_2.1.1.2.zip" + + version('2.1.1.2', '170e5b4a002277ff66866486da920693') + + depends_on('java', type=('build', 'run')) + depends_on('bcftools') + depends_on('bwa') + depends_on('samtools') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'PGDSpider{0}-cli.jar'.format(self.version.up_to(1)) + install(jar_file, prefix.bin) + + script_sh = join_path(os.path.dirname(__file__), "pgdspider.sh") + script = prefix.bin.pgdspider + install(script_sh, script) + set_executable(script) + + java = self.spec['java'].prefix.bin.java + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('pgdspider.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh b/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh new file mode 100644 index 0000000000..5ac0f66c08 --- /dev/null +++ b/var/spack/repos/builtin/packages/pgdspider/pgdspider.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the astral jar file +java $JAVA_ARGS $JAVA_OPTS -jar pgdspider.jar "$@" |