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braker & genemark-et: new packages (#5058)

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* braker & genemark-et: new packages

* fixing install
This commit is contained in:
Audrey Thoma 2017-08-10 20:04:37 -05:00 committed by Adam J. Stewart
parent 637f72a8fe
commit 2f29e9c18e
3 changed files with 106 additions and 0 deletions
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1
var/spack/repos/builtin/packages/augustus/package.py
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@ -32,6 +32,7 @@ class Augustus(MakefilePackage):
homepage = "http://bioinf.uni-greifswald.de/augustus/"
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz"
version('3.3', '9ebe494df78ebf6a43091cfc8551050c')
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
depends_on('bamtools')

52
var/spack/repos/builtin/packages/braker/package.py Normal file
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@ -0,0 +1,52 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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/BRAKER1_v1.11.tar.gz"
version('1.11', '297efe4cabdd239b710ac2c45d81f6a5')
depends_on('perl', type=('build', 'run'))
depends_on('augustus')
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)

53
var/spack/repos/builtin/packages/genemark-et/package.py Normal file
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@ -0,0 +1,53 @@
##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 *
import os
import glob
class GenemarkEt(Package):
"""Gene Prediction in Bacteria, archaea, Metagenomes and
Metatranscriptomes."""
homepage = "http://topaz.gatech.edu/GeneMark"
version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3')
depends_on('perl', type=('build', 'run'))
def url_for_version(self, version):
return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd())
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('gmes_petap'):
install_tree('lib', prefix.lib)
files = glob.iglob('*')
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix.lib)