09047d76e9
- add version 2.1.4 - change url to github - add perl dependencies - new version has a new source layout - filter shebang to use spack perl
67 lines
2.7 KiB
Python
67 lines
2.7 KiB
Python
# Copyright 2013-2019 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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from spack import *
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import os
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import glob
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class Braker(Package):
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"""BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
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that combines the advantages of GeneMark-ET and AUGUSTUS"""
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homepage = "http://exon.gatech.edu/braker1.html"
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url = "https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.4.tar.gz"
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list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
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version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52')
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version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
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version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
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url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-scalar-util-numeric', type=('build', 'run'))
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depends_on('perl-parallel-forkmanager', type=('build', 'run'))
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depends_on('perl-file-which', type=('build', 'run'))
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depends_on('perl-yaml', type=('build', 'run'))
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depends_on('perl-hash-merge', type=('build', 'run'))
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depends_on('perl-logger-simple', type=('build', 'run'))
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depends_on('perl-file-homedir', when='@2.1.4:', type=('build', 'run'))
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depends_on('augustus')
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depends_on('augustus@3.2.3', when='@:2.1.0')
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depends_on('genemark-et')
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depends_on('bamtools')
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depends_on('samtools')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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mkdirp(prefix.lib)
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if self.version < Version('2.1.2'):
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install('braker.pl', prefix.bin)
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install('filterGenemark.pl', prefix.bin)
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install('filterIntronsFindStrand.pl', prefix.bin)
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install('helpMod.pm', prefix.lib)
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else:
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install_tree('docs', prefix.docs)
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install_tree('example', prefix.example)
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with working_dir('scripts'):
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install('helpMod.pm', prefix.lib)
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files = glob.iglob('*.pl')
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for file in files:
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if os.path.isfile(file):
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install(file, prefix.bin)
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@run_after('install')
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def filter_sbang(self):
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with working_dir(self.prefix.bin):
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pattern = '^#!.*/usr/bin/env perl'
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repl = '#!{0}'.format(self.spec['perl'].command.path)
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files = glob.iglob("*.pl")
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for file in files:
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filter_file(pattern, repl, *files, backup=False)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PERL5LIB', prefix.lib)
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