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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
class Braker(Package):
"""BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
that combines the advantages of GeneMark-ET and AUGUSTUS"""
homepage = "http://exon.gatech.edu/braker1.html"
url = "https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.4.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
version('2.1.6', sha256='eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06')
version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52')
version('1.11', sha256='cb2d9abe1720ed58753d362eee4af3791007efc617754804882d31f9fe2eab00',
url='https://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
depends_on('perl', type=('build', 'run'))
depends_on('perl-scalar-util-numeric', type=('build', 'run'))
depends_on('perl-parallel-forkmanager', type=('build', 'run'))
depends_on('perl-file-which', type=('build', 'run'))
depends_on('perl-yaml', type=('build', 'run'))
depends_on('perl-hash-merge', type=('build', 'run'))
depends_on('perl-logger-simple', type=('build', 'run'))
depends_on('perl-file-homedir', when='@2.1.4:', type=('build', 'run'))
depends_on('augustus')
depends_on('augustus@3.2.3', when='@:2.1.0')
depends_on('genemark-et')
depends_on('bamtools')
depends_on('samtools')
depends_on('diamond')
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
if self.version < Version('2.1.2'):
install('braker.pl', prefix.bin)
install('filterGenemark.pl', prefix.bin)
install('filterIntronsFindStrand.pl', prefix.bin)
install('helpMod.pm', prefix.lib)
else:
install_tree('docs', prefix.docs)
install_tree('example', prefix.example)
with working_dir('scripts'):
install('helpMod.pm', prefix.lib)
install('*.pl', prefix.bin)
@run_after('install')
def filter_sbang(self):
with working_dir(self.prefix.bin):
pattern = '^#!.*/usr/bin/env perl'
repl = '#!{0}'.format(self.spec['perl'].command.path)
files = glob.iglob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
def setup_run_environment(self, env):
env.prepend_path('PERL5LIB', self.prefix.lib)
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