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orthofinder: Create new package. (#7364)

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lingnanyuan 2018-03-07 13:45:45 -06:00 committed by Massimiliano Culpo
parent ef310d9f66
commit f393a2c146
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var/spack/repos/builtin/packages/orthofinder/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 Orthofinder(Package):
"""OrthoFinder is a fast, accurate and comprehensive analysis tool for
comparative genomics.
It finds orthologues and orthogroups infers rooted gene trees for all
orthogroups and infers a rooted species tree for the species being
analysed. OrthoFinder also provides comprehensive statistics for
comparative genomic analyses. OrthoFinder is simple to use and all you
need to run it is a set of protein sequence files (one per species)
in FASTA format."""
homepage = "https://github.com/davidemms/OrthoFinder"
url = "https://github.com/davidemms/OrthoFinder/releases/download/2.2.0/OrthoFinder-2.2.0.tar.gz"
version('2.2.0', '4ff585e1eb148fc694a219296fbdd431')
depends_on('blast-plus', type='run')
depends_on('mcl', type='run')
depends_on('fastme', type='run')
depends_on('py-dlcpar', type='run')
def install(self, spec, prefix):
install_tree('.', prefix.bin)
chmod = which('chmod')
chmod('+x', join_path(prefix.bin, 'orthofinder'))