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

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")

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:")