##############################################################################
# Copyright (c) 2013-2018, 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 Busco(PythonPackage):
    """Assesses genome assembly and annotation completeness with Benchmarking
       Universal Single-Copy Orthologs"""

    homepage = "http://busco.ezlab.org/"
    url      = "https://gitlab.com/ezlab/busco"

    version('3.0.1', git='https://gitlab.com/ezlab/busco.git', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
    version('2.0.1', git='https://gitlab.com/ezlab/busco.git', commit='89aa1ab2527f03a87a214ca90a504ad236582a11')

    depends_on('python', type=('build', 'run'))
    depends_on('blast-plus')
    depends_on('hmmer')
    depends_on('augustus')

    def build(self, spec, prefix):
        if self.spec.satisfies('@2.0.1'):
            pass

    def install(self, spec, prefix):
        if self.spec.satisfies('@3.0.1'):
            with working_dir('scripts'):
                mkdirp(prefix.bin)
                install('generate_plot.py', prefix.bin)
                install('run_BUSCO.py', prefix.bin)
            install_tree('config', prefix.config)
            args = self.install_args(spec, prefix)
            self.setup_py('install', *args)
        if self.spec.satisfies('@2.0.1'):
            mkdirp(prefix.bin)
            install('BUSCO.py', prefix.bin)
            install('BUSCO_plot.py', prefix.bin)
