# 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 *


class PyAtropos(PythonPackage):
    """Atropos is tool for specific, sensitive, and speedy trimming of NGS
    reads. It is a fork of the venerable Cutadapt read trimmer."""

    homepage = "https://atropos.readthedocs.io"
    pypi = "atropos/atropos-1.1.22.tar.gz"
    git      = "https://github.com/jdidion/atropos.git"

    version('1.1.22', sha256='05e40cb9337421479c692e1154b962fbf811d7939b72c197a024929b7ae88b78')

    depends_on('python@3.3:', type=('build', 'run'))
    depends_on('py-setuptools', type=('build', 'run'))
    depends_on('py-cython@0.25.2:', type='build')
    depends_on('py-tqdm', type=('build', 'run'), when='+tqdm')
    depends_on('py-pysam', type=('build', 'run'), when='+pysam')

    variant('tqdm', default=False, description='Enable progress bar')
    variant('pysam', default=False, description='Enable bam file parsing')