##############################################################################
# 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 PyCheckmGenome(PythonPackage):
    """Assess the quality of microbial genomes recovered from isolates, single
    cells, and metagenomes"""

    homepage = "https://ecogenomics.github.io/CheckM"
    url      = "https://pypi.io/packages/source/c/checkm-genome/checkm-genome-1.0.11.tar.gz"

    version('1.0.11', '3058546ec324e2420cf72f0d2576114b')

    depends_on('hmmer@3.1b1:')
    depends_on('prodigal@2.6.1:')
    depends_on('py-numpy@1.8.0:',        type=('build', 'run'))
    depends_on('py-scipy@0.9.0:',        type=('build', 'run'))
    depends_on('py-matplotlib@1.3.1:',   type=('build', 'run'))
    depends_on('py-pysam@0.8.3:',        type=('build', 'run'))
    depends_on('py-dendropy@4.0.0:',     type=('build', 'run'))
