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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
from spack import *
class Orthofiller(Package):
"""OrthoFiller: Identifying missing annotations for evolutionarily
conserved genes."""
homepage = "https://github.com/mpdunne/orthofiller/"
url = "https://github.com/mpdunne/orthofiller/archive/1.1.4.tar.gz"
version('1.1.4', sha256='a693a3372a3f05041ce30cbf84da1be88e85eae4effe32dbd7809ccef119a295')
depends_on('augustus', type='run')
depends_on('bedtools2@2.25.0', type='run')
depends_on('hmmer', type='run')
depends_on('orthofinder', type='run')
depends_on('python@2.7:', type='run')
depends_on('py-biopython', type='run')
depends_on('py-scipy', type='run')
depends_on('r', type='run')
depends_on('r-gamlss', type='run')
depends_on('mafft', type='run')
def install(self, spec, prefix):
# orthofiller tests for common unix programs using man
# runtime modules will quickly overflow the maximum MANPATH;
# we change the man tests to use which instead, more reliable anyway
filter_file('"man "', '"which "', 'OrthoFiller.py', string=True)
os.chmod('OrthoFiller.py', 0o755)
mkdirp(prefix.bin)
install('OrthoFiller.py', prefix.bin)
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