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| -rw-r--r-- | var/spack/repos/builtin/packages/haploview/haploview.sh | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/haploview/package.py | 54 |
2 files changed, 57 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/haploview/haploview.sh b/var/spack/repos/builtin/packages/haploview/haploview.sh new file mode 100644 index 0000000000..0f6c60139c --- /dev/null +++ b/var/spack/repos/builtin/packages/haploview/haploview.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the haploview.jar file +java $JAVA_ARGS $JAVA_OPTS -jar haploview.jar "$@" diff --git a/var/spack/repos/builtin/packages/haploview/package.py b/var/spack/repos/builtin/packages/haploview/package.py new file mode 100644 index 0000000000..9ffe6898b5 --- /dev/null +++ b/var/spack/repos/builtin/packages/haploview/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 Haploview(Package): + """Haploview is designed to simplify and expedite the process of haplotype + analysis.""" + + homepage = "http://www.broadinstitute.org/haploview/haploview" + url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar" + + version('4.1', 'f7aa4accda5fad1be74c9c1969c6ee7d', expand=False) + + depends_on('java', type=('build', 'run')) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'Haploview{v}.jar'.format(v=self.version) + install(jar_file, prefix.bin) + + script_sh = join_path(os.path.dirname(__file__), "haploview.sh") + script = prefix.bin.haploview + 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('haploview.jar', join_path(prefix.bin, jar_file), + script, **kwargs) |