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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 PyHaphpipe(PythonPackage):
"""HAplotype and PHylodynamics pipeline for viral assembly,
population genetics, and phylodynamics."""
homepage = "https://github.com/gwcbi/haphpipe"
url = "https://github.com/gwcbi/haphpipe/archive/v1.0.3.tar.gz"
maintainers = ['dorton21']
version('1.0.3', sha256='9a9e8632a217ff4207c1dea66887a471e0ea04bbb7c0f0d72631acaba214bd37')
# Deps. taken from
# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/haphpipe/meta.yaml
# https://bioconda.github.io/recipes/haphpipe/README.html
# https://github.com/gwcbi/haphpipe/blob/master/environment.yml
depends_on('python@3.7:', type=('build', 'run'))
depends_on('py-future', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-biopython@1.73:', type=('build', 'run'))
depends_on('py-gsutil', type=('build', 'run'))
depends_on('py-sierrapy', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('bowtie2', type=('build', 'run'))
depends_on('blast-plus', type=('build', 'run'))
depends_on('freebayes', type=('build', 'run'))
depends_on('modeltest-ng', type=('build', 'run'))
depends_on('libdeflate', type=('build', 'run'))
depends_on('sratoolkit', type=('build', 'run'))
depends_on('spades', type=('build', 'run'))
depends_on('seqtk', type=('build', 'run'))
depends_on('raxml-ng~mpi', type=('build', 'run'))
depends_on('gatk@3.8-0', type=('build', 'run'))
depends_on('trinity', type=('build', 'run'))
depends_on('trimmomatic@0.38:', type=('build', 'run'))
depends_on('flash@1.2.11:', type=('build', 'run'))
depends_on('mummer@3.23:', type=('build', 'run'))
depends_on('bwa', type=('build', 'run'))
depends_on('samtools@1.9:', type=('build', 'run'))
depends_on('mafft', type=('build', 'run'))
depends_on('picard', type=('build', 'run'))
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