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

[Pjotr Prins <pjotr.public12@thebird.nl>]

I am at the biohackathon in Japan - planning to submit more of these.
Many people here are interested in our work :)

  http://2015.biohackathon.org/hackathon

OK, yes, it probably belongs in bioinformatics.scm. Note the gem
contains tests that pass ;). I love the abstraction that guix offers
for gems. I added to

  https://github.com/pjotrp/guix-notes/blob/master/RUBY.org#adding-a-ruby-gem-to-guix

Pj.

On Mon, Sep 14, 2015 at 10:01:40AM -0400, Thompson, David wrote:
> 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
> 

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