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authorLuke Diorio-Toth <ldioriototh@gmail.com>2022-10-20 15:44:57 -0500
committerGitHub <noreply@github.com>2022-10-20 15:44:57 -0500
commit9621b2bb3b226cc887c2a7a5b04e85e24c466f1a (patch)
tree9770c5d89feccadc069348c910fcd42ee4f0b6e1
parentee721f9c91a614b6dc6bacd3070f50cfeac97015 (diff)
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replaced package shortbred with py-shortbred (#33404)
* fixed version numbers to python 2 and old biopython * changed shortbred pacakge to pypi, removed python 2 version * added package description * re-added shortbred package with depreciated flag * fixed style and removed unnecessary python dep (it can't build with python 2 anyway) * removed whitespace and readded the python2.7.9+ dep * fixed style
-rw-r--r--var/spack/repos/builtin/packages/py-shortbred/package.py25
-rw-r--r--var/spack/repos/builtin/packages/shortbred/package.py6
2 files changed, 30 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/py-shortbred/package.py b/var/spack/repos/builtin/packages/py-shortbred/package.py
new file mode 100644
index 0000000000..44dc115f12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-shortbred/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2022 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 PyShortbred(PythonPackage):
+ """ShortBRED is a system for profiling protein families of interest at
+ very high specificity in shotgun meta'omic sequencing data."""
+
+ homepage = "https://huttenhower.sph.harvard.edu/shortbred/"
+ pypi = "shortbred/shortbred-0.9.5.tar.gz"
+
+ version("0.9.5", sha256="a6ac09b858f14e2c0b8622b122ec91e5d02d32c12429cad66626d7ef26df10d5")
+
+ depends_on("python@2.7.9:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-biopython@1.65:", type="run")
+ depends_on("blast-plus@2.2.28:", type="run")
+ depends_on("usearch@6.0.307:", type="run")
+ depends_on("muscle@3.8.31:", type="run")
+ depends_on("cdhit@4.6:", type="run")
diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py
index 502bfd32eb..a08fb3efc6 100644
--- a/var/spack/repos/builtin/packages/shortbred/package.py
+++ b/var/spack/repos/builtin/packages/shortbred/package.py
@@ -13,7 +13,11 @@ class Shortbred(Package):
homepage = "https://huttenhower.sph.harvard.edu/shortbred"
url = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
- version("0.9.4", sha256="a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba")
+ version(
+ "0.9.4",
+ sha256="a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba",
+ deprecated=True,
+ )
depends_on("blast-plus@2.2.28:")
depends_on("cdhit@4.6:")