##############################################################################
# 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 PyCnvkit(PythonPackage):
    """A command-line toolkit and Python library for detecting copy number
       variants and alterations genome-wide from high-throughput sequencing."""

    homepage = "http://cnvkit.readthedocs.io/en/stable/"
    url      = "https://github.com/etal/cnvkit/archive/v0.9.2.tar.gz"

    version('0.9.2', '16612c4dcc9570f6ef9fecc42caf1745')

    depends_on('py-setuptools',        type='build')
    depends_on('py-biopython@1.62:',   type=('build', 'run'))
    depends_on('py-future@0.15.2:',    type=('build', 'run'))
    depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
    depends_on('py-numpy@1.9:',        type=('build', 'run'))
    depends_on('py-pandas@0.18.1:',    type=('build', 'run'))
    depends_on('py-pyfaidx@0.4.7:',    type=('build', 'run'))
    depends_on('py-pysam@0.10.0:0.13', type=('build', 'run'))
    depends_on('py-reportlab@3.0:',    type=('build', 'run'))
    depends_on('py-scipy@0.15.0:',     type=('build', 'run'))
    depends_on('bcftools@1.6',         type=('build', 'run'))
    depends_on('samtools@1.6',         type=('build', 'run'))
