1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
# 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 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")
# renamed to getorganelle
version(
"1.7.5.0",
sha256="c498196737726cb4c0158f23037bf301a069f5028ece729bb4d09c7d915df93d",
deprecated=True,
)
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)
|
