[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
01/06: gnu: Add python-pyspoa.
From: |
guix-commits |
Subject: |
01/06: gnu: Add python-pyspoa. |
Date: |
Thu, 21 Oct 2021 09:41:49 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 6526c35df5d96a3020fdad8bbe4240ca8b2954ee
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Oct 21 11:43:48 2021 +0000
gnu: Add python-pyspoa.
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
---
gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7dec74f..afbacc1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15065,6 +15065,53 @@ line, interactively explore genomic data within
Jupyter environment or web
browser.")
(license license:gpl3+)))
+(define-public python-pyspoa
+ (package
+ (name "python-pyspoa")
+ (version "0.0.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/nanoporetech/pyspoa")
+ (commit (string-append "v" version))
+ (recursive? #true)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1lgf2shzhxkcsircd6vy46h27pjljd5q95fyz1cm3lkk702qbnzx"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'build-libspoa
+ (lambda _
+ (mkdir-p "src/build")
+ (with-directory-excursion "src/build"
+ (invoke "cmake"
+ "-Dspoa_optimize_for_portability=ON"
+ "-DCMAKE_BUILD_TYPE=Release"
+ "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\"
-fPIC"
+ "..")
+ (invoke "make"))))
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "python" "tests/test_pyspoa.py")))))))
+ (propagated-inputs
+ `(("pybind11" ,pybind11)))
+ (native-inputs
+ `(("cmake" ,cmake-minimal)))
+ (home-page "https://github.com/nanoporetech/pyspoa")
+ (synopsis "Python bindings for the SIMD partial order alignment library ")
+ (description
+ "This package provides Python bindings for spoa, a C++ implementation of
+the @dfn{partial order alignment} (POA) algorithm (as described in
+10.1093/bioinformatics/18.3.452) which is used to generate consensus
+sequences")
+ (license license:expat)))
+
(define-public scregseg
(package
(name "scregseg")
- branch master updated (ac327cc -> 42c9b75), guix-commits, 2021/10/21
- 02/06: gnu: Add python-bwapy., guix-commits, 2021/10/21
- 03/06: gnu: instrain: Update to 1.5.4., guix-commits, 2021/10/21
- 01/06: gnu: Add python-pyspoa.,
guix-commits <=
- 05/06: gnu: python-biopython: Update to 1.76., guix-commits, 2021/10/21
- 06/06: gnu: Add ciri-long., guix-commits, 2021/10/21
- 04/06: gnu: python-levenshtein: Update to 0.12.2., guix-commits, 2021/10/21