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| -rw-r--r-- | var/spack/repos/builtin/packages/rna-seqc/package.py | 63 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh | 3 |
2 files changed, 66 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py new file mode 100644 index 0000000000..389a96d428 --- /dev/null +++ b/var/spack/repos/builtin/packages/rna-seqc/package.py @@ -0,0 +1,63 @@ +############################################################################## +# 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 +############################################################################## +from spack import * +from shutil import copyfile +import os.path + + +class RnaSeqc(Package): + """RNA-SeQC is a java program which computes a series of quality control + metrics for RNA-seq data.""" + + homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc" + url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar" + + version('1.1.8', '71d7b5d3b3dcc1893cdc7f6819185d41', expand=False) + version('1.1.7', '2d0b8ecac955af2f9bc1b185fdfb6b45', expand=False) + version('1.1.6', 'fa9c9885081ae2e47f285c7c0f596a14', expand=False) + version('1.1.5', '4b875671e906f708cbb8fd9bcf0e958d', expand=False) + version('1.1.4', 'b04d06947c48cb2dc1b0ba29c8232db5', expand=False) + + depends_on('jdk@8:', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted) + install(jar_file, 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__), "rna-seqc.sh") + script = join_path(prefix.bin, "rna-seqc") + 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['jdk'].prefix, 'bin', 'java') + kwargs = {'ignore_absent': False, 'backup': False, 'string': False} + filter_file('^java', java, script, **kwargs) + filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file), + script, **kwargs) diff --git a/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh new file mode 100644 index 0000000000..6f3d22cbf9 --- /dev/null +++ b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the rna-seqc jar file +java -jar RNA-SeQC_v{}.jar "$@" |