24c01d57cf
* fix remaining flake8 errors * imports: sort imports everywhere in Spack We enabled import order checking in #23947, but fixing things manually drives people crazy. This used `spack style --fix --all` from #24071 to automatically sort everything in Spack so PR submitters won't have to deal with it. This should go in after #24071, as it assumes we're using `isort`, not `flake8-import-order` to order things. `isort` seems to be more flexible and allows `llnl` mports to be in their own group before `spack` ones, so this seems like a good switch.
49 lines
1.7 KiB
Python
49 lines
1.7 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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from spack import *
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class Guidance(MakefilePackage):
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"""Guidance: Accurate detection of unreliable alignment regions accounting
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for the uncertainty of multiple parameters."""
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homepage = "http://guidance.tau.ac.il/ver2/"
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url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
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version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-bioperl', type=('build', 'run'))
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depends_on('ruby')
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depends_on('prank')
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depends_on('clustalw')
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depends_on('mafft')
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depends_on('muscle')
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conflicts('%gcc@6.2.0:')
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def edit(self, spec, prefix):
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for dir in 'Guidance', 'Selecton', 'bioSequence_scripts_and_constants':
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with working_dir(join_path('www', dir)):
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files = glob.iglob('*.pl')
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for file in files:
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perl = FileFilter(file)
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perl.filter('#!/usr/bin/perl -w', '#!/usr/bin/env perl')
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def install(self, spac, prefix):
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mkdir(prefix.bin)
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install_tree('libs', prefix.bin.libs)
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install_tree('programs', prefix.bin.programs)
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install_tree('www', prefix.bin.www)
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with working_dir(join_path('www', 'Guidance')): # copy without suffix
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install('guidance.pl', join_path(prefix.bin.www.Guidance,
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'guidance'))
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def setup_run_environment(self, env):
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env.prepend_path('PATH', prefix.bin.www.Guidance)
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