Re: [PATCH] gnu: Add ruby-bio-locus.

["Thompson, David" <dthompson2@worcester.edu>]

On Mon, Sep 14, 2015 at 9:24 AM, Pjotr Prins <pjotr.public12@thebird.nl> wrote:
> * gnu/packages/ruby.scm (ruby-bio-locus): New variable.

Awesome!  Just a couple of minor comments below.

> ---
>  gnu/packages/ruby.scm | 20 ++++++++++++++++++++
>  1 file changed, 20 insertions(+)
>
> diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
> index ee0acc8..0a0fc1a 100644
> --- a/gnu/packages/ruby.scm
> +++ b/gnu/packages/ruby.scm
> @@ -1124,3 +1124,23 @@ it unifies the API for web servers, web frameworks, and software in between
>  into a single method call.")
>      (home-page "http://rack.github.io/")
>      (license license:expat)))
> +
> +(define-public ruby-bio-locus
> +  (package
> +    (name "ruby-bio-locus")

This is an application, not a library, correct?  If so, I think it
would be best to name it just "bio-locus" and put it in the (gnu
packages bioinformatics) module.  WDYT?

> +    (version "0.0.7")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (rubygems-uri "bio-locus" version))
> +       (sha256
> +        (base32
> +         "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
> +    (build-system ruby-build-system)
> +    (native-inputs
> +     `(("ruby-rspec" ,ruby-rspec)))
> +    (synopsis "Tool for fast querying of genome locations")
> +    (description "This tabix-like tool essentially allows your to
> +store this chr+pos or chr+pos+alt information in a fast database.")

How about something more descriptive?  Here's a modified snippet from
your README:

    Bio-locus is a tool for fast querying of genome locations.
    Many file formats in bioinformatics contain records that start with a
    chromosome name and a position for a SNP, or a start-end position
for indels.
    Bio-locus allows users to store this chr+pos or chr+pos+alt information in a
    fast database.

> +    (home-page "https://github.com/pjotrp/bio-locus")
> +    (license license:expat)))
> --
> 2.4.3
>

Thanks!  Keep 'em coming!

- Dave