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# Copyright 2013-2018 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)
from spack import *
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 = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
url='http://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('augustus@3.2.3')
depends_on('genemark-et')
depends_on('bamtools')
depends_on('samtools')
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
install('braker.pl', prefix.bin)
install('filterGenemark.pl', prefix.bin)
install('filterIntronsFindStrand.pl', prefix.bin)
install('helpMod.pm', prefix.lib)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix.lib)
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