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.
57 lines
2.3 KiB
Python
57 lines
2.3 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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class Snphylo(Package):
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"""A pipeline to generate a phylogenetic tree from huge SNP data"""
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homepage = "http://chibba.pgml.uga.edu/snphylo/"
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url = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
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version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
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depends_on('python', type=('build', 'run'))
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depends_on('r', type=('build', 'run'))
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depends_on('r-phangorn', type=('build', 'run'))
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depends_on('r-gdsfmt', type=('build', 'run'))
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depends_on('r-snprelate', type=('build', 'run'))
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depends_on('r-getopt', type=('build', 'run'))
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depends_on('muscle')
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depends_on('phylip')
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def install(self, spec, prefix):
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install_answer = ['y', 'y', 'y', 'y']
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install_answer_input = 'spack-config.in'
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with open(install_answer_input, 'w') as f:
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f.writelines(install_answer)
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with open(install_answer_input, 'r') as f:
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bash = which('bash')
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bash('./setup.sh', input=f)
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install_tree('.', prefix)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PATH', self.spec.prefix)
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