diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2015-09-19 19:31:57 +1000 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-09-25 16:16:28 +0200 |
| commit | d708b7a9734e5a2b2bd9db6152b2584e01086517 (patch) | |
| tree | ce48cb1be4fd3497468eadad30b60e93941efc94 /gnu/packages/bioinformatics.scm | |
| parent | 665ce1ebe548c71e9da54caeb62eca5f9f588d4d (diff) | |
gnu: Add seqmagick.
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2e31d85b2d..e647186ab3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2552,6 +2552,44 @@ manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.") (license license:bsd-3))) +(define-public seqmagick + (package + (name "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-biopython" ,python2-biopython))) + (native-inputs + `(("python-setuptools" ,python2-setuptools) + ("python-nose" ,python2-nose))) + (home-page "http://github.com/fhcrc/seqmagick") + (synopsis "Tools for converting and modifying sequence files") + (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") |