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| -rw-r--r-- | var/spack/repos/builtin/packages/qorts/QoRTs.sh | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/qorts/package.py | 71 |
2 files changed, 74 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/qorts/QoRTs.sh b/var/spack/repos/builtin/packages/qorts/QoRTs.sh new file mode 100644 index 0000000000..d847e76e05 --- /dev/null +++ b/var/spack/repos/builtin/packages/qorts/QoRTs.sh @@ -0,0 +1,3 @@ +#!/bin/sh +# convenience wrapper for the QoRTs jar file +java -jar QoRTs.jar "$@" diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py new file mode 100644 index 0000000000..bb71f15b8f --- /dev/null +++ b/var/spack/repos/builtin/packages/qorts/package.py @@ -0,0 +1,71 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 * +import os.path +from shutil import copyfile + + +class Qorts(RPackage): + """The QoRTs software package is a fast, efficient, and portable + multifunction toolkit designed to assist in the analysis, quality + control, and data management of RNA-Seq and DNA-Seq datasets. Its + primary function is to aid in the detection and identification of + errors, biases, and artifacts produced by high-throughput sequencing + technology.""" + + homepage = "https://github.com/hartleys/QoRTs" + url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz" + + version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829') + + depends_on('java', type='run') + + resource( + name='QoRTs.jar', + url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar', + md5='918df4291538218c12caa3ab98c535e9', + placement='jarfile', + expand=False + ) + + @run_after('install') + def install_jar(self): + install_tree(join_path(self.stage.source_path, 'jarfile'), + self.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__), "QoRTs.sh") + script = self.prefix.bin.QoRTs + copyfile(script_sh, script) + set_executable(script) + + # Munge the helper script to explicitly point to java and the + # jar file. + java = self.spec['java'].prefix.bin.java + kwargs = {'backup': False} + filter_file('^java', java, script, **kwargs) + filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'), + script, **kwargs) |