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##############################################################################
# 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
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
install(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)
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