Re: [PATCH] gnu: Add TopHat.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

On 19/01/16 23:52, Ricardo Wurmus wrote:
> Hi Guix,
>
> 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.
>
> 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 seqan@1.4.2 and samtools@0.1.19.  A
> snippet removes the bundled sources.
>
> An additional patch to the sources makes it possible to build TopHat
> with SeqAn 1.4.2.
Excellent.
> +    ;; 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."))))
Am I right in thinking that the only other license used is asl2.0 ? If 
so why not say so?

Other than that, looks pretty good.

Thanks for packaging these important bioinformatics tools.
ben