9653dc2aac
* r-qorts: Create new package. * Change dependency to java, change package name. * Remove some join_path.
72 lines
2.9 KiB
Python
72 lines
2.9 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import os.path
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from shutil import copyfile
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class Qorts(RPackage):
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"""The QoRTs software package is a fast, efficient, and portable
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multifunction toolkit designed to assist in the analysis, quality
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control, and data management of RNA-Seq and DNA-Seq datasets. Its
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primary function is to aid in the detection and identification of
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errors, biases, and artifacts produced by high-throughput sequencing
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technology."""
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homepage = "https://github.com/hartleys/QoRTs"
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url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
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version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829')
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depends_on('java', type='run')
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resource(
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name='QoRTs.jar',
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url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
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md5='918df4291538218c12caa3ab98c535e9',
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placement='jarfile',
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expand=False
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)
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@run_after('install')
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def install_jar(self):
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install_tree(join_path(self.stage.source_path, 'jarfile'),
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self.prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
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script = self.prefix.bin.QoRTs
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copyfile(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = self.spec['java'].prefix.bin.java
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kwargs = {'backup': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
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script, **kwargs)
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