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-rw-r--r--var/spack/repos/builtin/packages/getorganelle/package.py34
-rw-r--r--var/spack/repos/builtin/packages/py-getorganelle/package.py7
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"))