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| author | Luke Diorio-Toth <ldioriototh@gmail.com> | 2022-10-20 15:44:57 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-10-20 15:44:57 -0500 |
| commit | 9621b2bb3b226cc887c2a7a5b04e85e24c466f1a (patch) | |
| tree | 9770c5d89feccadc069348c910fcd42ee4f0b6e1 /var | |
| parent | ee721f9c91a614b6dc6bacd3070f50cfeac97015 (diff) | |
| download | spack-9621b2bb3b226cc887c2a7a5b04e85e24c466f1a.tar.gz spack-9621b2bb3b226cc887c2a7a5b04e85e24c466f1a.tar.bz2 spack-9621b2bb3b226cc887c2a7a5b04e85e24c466f1a.tar.xz spack-9621b2bb3b226cc887c2a7a5b04e85e24c466f1a.zip | |
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
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/py-shortbred/package.py | 25 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/shortbred/package.py | 6 |
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:") |