Re: [PATCH] gnu: Add TopHat.

[Ludovic Courtès]

Ricardo Wurmus <address@hidden> skribis:

> I’m happy to be able to submit a patch to add TopHat.  It’s a very
> popular piece of bioinformatics software that I didn’t submit to Guix
> upstream before as the license wasn’t clear.  The latest release at that
> time contained a LICENSE file with the text of the Artistic license 1.0.
>
> The new 2.1.0 release no longer contains this file; instead it declares
> the license to be the Boost Software license 1.0.  Additionally, the
> license has been clarified on a Github issue (which I linked to).  I
> only just noticed this because a user asked me to package the latest
> version and I was very happy to see the Artistic license removed.

One more free software package, this is good news!

> The sources of TopHat bundle the SeqAn header library (version 1.3) and
> the sources of samtools 0.1.18.  I’m patching the Makefile in a build
> phase to use our packages for address@hidden and address@hidden  A
> snippet removes the bundled sources.

Good.

> From 91f7bacd8657b4be6669a2e72a2ca74b2e44a62f Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <address@hidden>
> Date: Tue, 19 Jan 2016 14:29:19 +0100
> Subject: [PATCH] gnu: Add TopHat.
>
> * gnu/packages/bioinformatics.scm (tophat): New variable.
> * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
> * gnu-system.am (dist_patch_DATA): Add it.

[...]

> +    (synopsis "Spliced read mapper for RNA-Seq")
> +    (description
> +     "TopHat is a fast splice junction mapper for RNA-Seq reads.  It aligns

It would be nice to contextualize a bit, for instance by adding a word
after “RNA-Seq”, like:

  … for RNA-Seq bioinformatics foobars

or:

  … for the RNA-Seq bioinformatics thingie

Something like that.  :-)

> +    ;; TopHat is released under the Boost Software License, Version 1.0
> +    ;; See 
> https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
> +    (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt";
> +                                "Some components have other similar 
> licences."))))

You can use ‘license:boost1.0’ here.

Otherwise LGTM, thanks!

Ludo’.