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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)
import os
import shutil
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/2.5.2/OrthoFinder_source.tar.gz"
version('2.5.2', sha256='e0752b66866e23a11f0592e880fac5f67258f9cf926f926dec8849564c41b8f7')
version('2.2.0', sha256='375f711086b44e2118d7d460821294744245e254e5fa2151dfe73100c0707a8c')
depends_on('py-numpy', type='run')
depends_on('py-scipy', type='run')
depends_on('diamond', type='run')
depends_on('blast-plus', type='run')
depends_on('mcl', type='run')
depends_on('fastme', type='run')
def url_for_version(self, version):
if '@:2.3.6' in self.spec:
url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder-{0}_source.tar.gz"
return url.format(version)
else:
url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder_source.tar.gz"
return url.format(version)
def install(self, spec, prefix):
if '@2.2.0' in spec:
install_tree('./orthofinder', prefix.bin)
else:
install_tree('.', prefix.bin)
shutil.rmtree(prefix.bin.scripts_of.bin)
os.rename('%s/orthofinder.py' % prefix.bin, '%s/orthofinder' % prefix.bin)
def setup_run_environment(self, env):
env.prepend_path('PATH', prefix.bin)
env.prepend_path('PATH', prefix.bin.tools)
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