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# Copyright 2013-2022 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')
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