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| author | snehring <7978778+snehring@users.noreply.github.com> | 2023-02-02 13:13:32 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-02-02 13:13:32 -0600 |
| commit | defa4a2340f6231655c51cbae711bc5ebd2d4b45 (patch) | |
| tree | d27b1cfda62363693657bdd39d2d1b1d56d3ee48 /var | |
| parent | 1e1d1ec43b1aa0ea5eb2390f20e24f5afc6eb158 (diff) | |
| download | spack-defa4a2340f6231655c51cbae711bc5ebd2d4b45.tar.gz spack-defa4a2340f6231655c51cbae711bc5ebd2d4b45.tar.bz2 spack-defa4a2340f6231655c51cbae711bc5ebd2d4b45.tar.xz spack-defa4a2340f6231655c51cbae711bc5ebd2d4b45.zip | |
py-getorganelle: rename to getorganelle and add version 1.7.7.0 (#35270)
* py-getorganelle: rename to getorganelle and add version 1.7.7.0
* py-getorganelle: deprecating package
Diffstat (limited to 'var')
| -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")) |