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New package: getOrganelle@1.7.5.0 (#25725)

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Desmond Orton 2021-09-03 16:04:24 -05:00 committed by GitHub
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var/spack/repos/builtin/packages/py-getorganelle/package.py Normal file
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# 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 PyGetorganelle(PythonPackage):
"""Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)"""
homepage = "https://github.com/Kinggerm/GetOrganelle"
url = "https://github.com/Kinggerm/GetOrganelle/archive/refs/tags/1.7.5.0.tar.gz"
maintainers = ['dorton21']
version('1.7.5.0', sha256='c498196737726cb4c0158f23037bf301a069f5028ece729bb4d09c7d915df93d')
depends_on('py-setuptools', type='build')
depends_on('py-numpy@1.16.4:', type=('build', 'run'))
depends_on('py-scipy@1.3.0:', type=('build', 'run'))
depends_on('py-sympy@1.4:', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('bowtie2', type='run')
depends_on('spades', type='run')
depends_on('blast-plus', type='run')
# Allow access to relevant runtime scripts
# I.e. get_organelle_config.py, get_organelle_from_reads.py, etc.
def setup_run_environment(self, env):
env.prepend_path('PATH', prefix)
env.prepend_path('PATH', prefix.Utilities)