Hi Ben, thank you very much for your patch!
> 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. Maybe this should be just called “seqmagick”. It’s written in Python, but since it’s not a library I don’t think it needs to have the “python2-” prefix. > +(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) I think this should be a native input instead. > + ("python-biopython" ,python2-biopython))) And this looks like it should be a propagated input instead. Have you tried running seqmagick after installing it with this package recipe? I found that Python executables often require either propagated inputs or wrapping in PYTHONPATH to work without runtime errors. > + (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") The synopsis is a bit long. You could shave off two words like this: “Command-line tools for converting and modifying sequence files” but that’s not really much better. I’m open to suggestions. > + (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))) > + I’m not sure if it’s really “GPLv3 only” or “GPLv3 or later” as there are no license headers anywhere. Maybe others could comment what’s the proper declaration here. ~~ Ricardo
