[BioRuby] tutorial

Pjotr Prins pjotr.public14 at thebird.nl
Thu Mar 3 19:12:46 UTC 2011

Thanks Peter and Chris. I am glad we can learn from your experience.

Toshiaki had a very cool idea today (on IRC). The implications
carry beyond BioRuby gems. 

My wish is to see whether BioRuby and plugins are running well on
different Ruby implementations, and operating systems.

The reality is that developers won't test every possibility.

On the other hand, users do ;)

Also, for every plugin and BioRuby we create tests.

Users can run those tests. 

So, what we need is a tool to report test results to some central DB

If any user can simply run a test - say bioruby/test/test_any1.rb - we
could ask them (or they can choose to do it themselves) and
automatically update the DB centrally through a web service.

  biogem --report-test test/test_any1.rb

Resulting in:

  BioRuby, test_any1.rb runs on ruby 1.9.2p136 (2010-12-25 revision 30365) [i686-linux]

or, worse scenario, fail with trace ;)

We could pass in more info (dependencies etc). 

Not too hard to implement, and a great resource for docs and feedback
to users.

This would be interesting to rubygems in general. Debian uses
something similar for packages. What do you think? I don't think
BioPerl or BioPython has that, correct?


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