Re: [PATCH] gnu: Add freebayes.

[Leo Famulari]

On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:

Thanks for the patch! This looks like a big one!

[...]

> +      (native-inputs
> +       `(("cmake" ,cmake)
> +         ("htslib" ,htslib)
> +         ("zlib" ,zlib)
> +         ("python" ,python-2)
> +         ("perl" ,perl)
> +         ("bamtools-src"
> +          ,(origin
> +             (method url-fetch)
> +             (uri (string-append "https://github.com/ekg/bamtools/archive/";
> +                  "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz"))
> +             (file-name "bamtools-src.tar.gz")
> +             (sha256
> +              (base32 
> "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1"))))

[... more sub-modules ...]

> +      (arguments
> +       `(#:tests? #f

Can you say why tests are disabled? It can be as simple as "no test
suite".

> +         #:phases
> +         (modify-phases %standard-phases
> +           (delete 'configure)
> +           (delete 'check)

This can be removed when using "#:tests? #f", which is the preferred way
to skip tests.

[...]

> Dear Guix,
> 
> I have a patch to add another bioinformatics tool: FreeBayes. It is a
> rather long patch, so suspect it isn't completely 'guix-proof'.
> 
> One of the problems with the patch is probably the bulk of dependencies
> dragged in (for example, vcflib).  They use specific versions so they
> are tied to this package (so that's why I cannot package them separately).

You can specify the version of dependencies when you list them in your
package. There is an example of this in the package definition of
fltk [0]. Is that not an appropriate solution for freebayes?

In any case, I think we should find some way to specify the license of
the code in all those modules.

I think somebody with some more experience should weigh in...

Cc-ing Ricardo since he also packages a lot of bioinformatics packages.

Thanks again for putting such a complicated patch together! We will find
the best way to add freebayes to the distribution :)

[0] Due to a recent change, the most correct method of specifying the
version uses '@' to separate the package name and version rather than
'-'.