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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)
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', sha256='7314f3fdfb24d84aa5b9ee27ce9f670df314889c12b8100e4e476c2d21a1c8e7')
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'))
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