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replaced package shortbred with py-shortbred (#33404)

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* 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
This commit is contained in:
Luke Diorio-Toth 2022-10-20 15:44:57 -05:00 committed by GitHub
parent ee721f9c91
commit 9621b2bb3b
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2 changed files with 30 additions and 1 deletions
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25
var/spack/repos/builtin/packages/py-shortbred/package.py Normal file
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@ -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")

6
var/spack/repos/builtin/packages/shortbred/package.py
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@ -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:")