Thanks in advance for review peoples.
>From 298c9aabc2d042c45c8f96d83229016dc5c1cbd6 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Thu, 17 Sep 2015 21:43:12 +1000
Subject: [PATCH] gnu: Add python2-seqmagick.
* gnu/packages/bioinformatics.scm (python2-seqmagick): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03eb2df..cffe0e9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2489,6 +2489,45 @@ manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
+(define-public python2-seqmagick
+ (package
+ (name "python2-seqmagick")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-";
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
+ (build-system python-build-system)
+ (arguments
+ ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ ;; current test in setup.py does not work as of 0.6.1,
+ ;; so use nose to run tests instead for now. See
+ ;; https://github.com/fhcrc/seqmagick/issues/55
+ (replace 'check (lambda _ (zero? (system* "nosetests")))))))
+ (inputs
+ `(("python-setuptools" ,python2-setuptools)
+ ("python-biopython" ,python2-biopython)))
+ (native-inputs
+ `(("python-nose" ,python2-nose)))
+ (home-page "http://github.com/fhcrc/seqmagick";)
+ (synopsis
+ "Tools for converting and modifying sequence files from the command-line")
+ (description
+ "Bioinformaticians often have to convert sequence files between formats
+and do little manipulations on them, and it's not worth writing scripts for
+that. Seqmagick is a utility to expose the file format conversion in
+BioPython in a convenient way. Instead of having a big mess of scripts, there
+is one that takes arguments.")
+ (license license:gpl3)))
+
(define-public star
(package
(name "star")
--
2.4.3
