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.
52 lines
1.9 KiB
Python
52 lines
1.9 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 os import chmod
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from spack import *
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class Mirdeep2(Package):
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"""miRDeep2 is a completely overhauled tool which discovers microRNA genes
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by analyzing sequenced RNAs."""
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homepage = "https://www.mdc-berlin.de/8551903/en/"
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url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
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version('0.0.8', sha256='eeb24ee1b0e76b49ee2f542da3ee7d46d163c80b152709e963492b79f4fca1b8')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-pdf-api2', type=('build', 'run'))
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depends_on('bowtie')
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depends_on('viennarna')
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depends_on('squid')
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depends_on('randfold')
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def url_for_version(self, version):
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url = 'https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip'
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return url.format(version.underscored)
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def patch(self):
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with working_dir('src'):
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files = glob.iglob("*.pl")
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for file in files:
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chmod(file, 0o755)
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change = FileFilter(file)
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change.filter('usr/bin/perl', 'usr/bin/env perl')
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change.filter('perl -W', 'perl')
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change.filter("../Rfam_for_miRDeep.fa",
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"Rfam_for_miRDeep.fa")
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change.filter("../install_successful",
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"install_successful")
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def install(self, spec, prefix):
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install_tree('src', prefix.bin)
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install('Rfam_for_miRDeep.fa', prefix.bin)
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# miRDeep looks for the install_sucessful file to check if you used
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# their automated install script which we'll just be kind of hacking
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# around
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touch(prefix.bin.install_successful)
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