# 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 *
import os


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)