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# Copyright 2013-2023 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.package import *
class Getorganelle(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("snehring")
version("1.7.7.0", sha256="dd351b5cd33688adfcd8bff9794ae0cc0ce01a572dac2bcf6c9d7db77b3e4883")
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)
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