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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os.path
from spack import *
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', sha256='c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08')
depends_on('java', type='run')
resource(
name='QoRTs.jar',
url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
sha256='e808d2e05c67ee41eee605b7821aafa7ae894288ebb01d8b1bfb136970c801ce',
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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