diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/getorganelle/package.py | 34 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/py-getorganelle/package.py | 7 |
2 files changed, 40 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/getorganelle/package.py b/var/spack/repos/builtin/packages/getorganelle/package.py new file mode 100644 index 0000000000..5a87eacf6d --- /dev/null +++ b/var/spack/repos/builtin/packages/getorganelle/package.py @@ -0,0 +1,34 @@ +# 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) diff --git a/var/spack/repos/builtin/packages/py-getorganelle/package.py b/var/spack/repos/builtin/packages/py-getorganelle/package.py index 2c5b9ba1d4..aebb767706 100644 --- a/var/spack/repos/builtin/packages/py-getorganelle/package.py +++ b/var/spack/repos/builtin/packages/py-getorganelle/package.py @@ -14,7 +14,12 @@ class PyGetorganelle(PythonPackage): maintainers("dorton21") - version("1.7.5.0", sha256="c498196737726cb4c0158f23037bf301a069f5028ece729bb4d09c7d915df93d") + # 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")) |