73c978ddd9
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`. - `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory. - `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory. - `install` and `copy` are analogous single-file functions. - add more extensive tests for these functions - update packages to use these functions.
64 lines
2.7 KiB
Python
64 lines
2.7 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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class Trimmomatic(Package):
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"""A flexible read trimming tool for Illumina NGS data."""
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homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
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url = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
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# Older version aren't explicitly made available, but the URL
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# works as we'd like it to, so...
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version('0.36', '8549130d86b6f0382b1a71a2eb45de39')
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version('0.33', '924fc8eb38fdff71740a0e05d32d6a2b')
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depends_on('java@8:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'trimmomatic-{v}.jar'.format(v=self.version.dotted)
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install(jar_file, prefix.bin)
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# Put the adapter files someplace sensible
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install_tree('adapters', prefix.share.adapters)
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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__), "trimmomatic.sh")
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script = prefix.bin.trimmomatic
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install(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 = {'ignore_absent': False, 'backup': False, 'string': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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