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Re: [PATCH] gnu: Add ruby-bio-locus.
From: |
Pjotr Prins |
Subject: |
Re: [PATCH] gnu: Add ruby-bio-locus. |
Date: |
Mon, 14 Sep 2015 16:18:52 +0200 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
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 <address@hidden> 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
>
--