7c06492d94
* braker: add new version 2.1.0 * Set verison in descending order. * Update URL. * url * braker: change url format.
56 lines
2.3 KiB
Python
56 lines
2.3 KiB
Python
##############################################################################
|
|
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
|
|
# Produced at the Lawrence Livermore National Laboratory.
|
|
#
|
|
# This file is part of Spack.
|
|
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
|
# LLNL-CODE-647188
|
|
#
|
|
# For details, see https://github.com/spack/spack
|
|
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
|
|
#
|
|
# This program is free software; you can redistribute it and/or modify
|
|
# it under the terms of the GNU Lesser General Public License (as
|
|
# published by the Free Software Foundation) version 2.1, February 1999.
|
|
#
|
|
# This program is distributed in the hope that it will be useful, but
|
|
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
|
|
# conditions of the GNU Lesser General Public License for more details.
|
|
#
|
|
# You should have received a copy of the GNU Lesser General Public
|
|
# License along with this program; if not, write to the Free Software
|
|
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
|
##############################################################################
|
|
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('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)
|