[BioRuby] biogems.info and some newish gems

[Pjotr Prins]

Hi Matt,

Are these gems on rubygems.org? I am getting:

  ERROR:  No gem matching 'sqed (>= 0)' found
  ./bin/fetch-geminfo.rb:204:in `block in <main>': Response code for sqed is 404 (Exception)

Pj.

On Sun, Sep 28, 2014 at 10:41:46AM -0500, Matt Yoder wrote:
> Hi all,
> 
> A coupe notes.  I'm wondering if the about statement "Biogems are
> automatically listed at biogems.info when the gem is pushed to
> rubygems.org, using the biogem tool, and the name of the gem starts
> with bio- (bio dash), e.g. bio-fasta or bio-gff3. " is presently true?
>  There are many gems listed that don't start with bio-, and while I
> haven't looked too closely I suspect some also did not use the biogem
> tool? How are these getting on the list?
> 
> For reference, here's a number of gems I've worked on.  They are
> variously polished!
> 
> https://github.com/mjy/obo_parser
> https://github.com/mjy/nexus_parser
> https://github.com/mjy/rubyMorphbank
> 
> and, more recently, with my new group (some of these very rough, in dev)
> 
> https://github.com/SpeciesFileGroup/taxonifi
> https://github.com/SpeciesFileGroup/ref2bibtex
> https://github.com/SpeciesFileGroup/sqed
> https://github.com/SpeciesFileGroup/rubyBHL
> 
> Finally, perhaps of most interest, developed recently at the open tree
> hackathon:
> 
> https://github.com/SpeciesFileGroup/bark
> 
> And a shameless plug for a new Rails project that will use many if not
> all of these gems: http://taxonworks.org.  We'd love to have input on
> any and all projects, and I'd be happy to answer any questions about
> these efforts.
> 
> Cheers,
> Matt Yoder
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