Re: [PATCH] Add python2-seqmagick.

[Ricardo Wurmus]

Hi Ben,

thank you very much for your patch!

> From 298c9aabc2d042c45c8f96d83229016dc5c1cbd6 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <address@hidden>
> 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