[BioRuby] Guidelines for writing bioruby plugins
pjotr.public14 at thebird.nl
Sat Oct 9 09:05:26 UTC 2010
The plugin system is in a conceptual stage. I intend to write an
'Anatomy of a BioRuby plugin' soon. Some quick responses
On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote:
> Hi Bioruby developers,
> I have heard of bioruby plugins and also seen two such plugins from github
> http://github.com/pjotrp/bioruby-gff3-plugin and
> 1. Is the plugin system supposed to open development methods? (helios
> uses unit testing while pjotrp uses r-spec for testing)
You are free to choose
> 2. Will the core developers concentrate on making bioruby core more stable?
That is the goal
> 3. What constitutes Bioruby core?
Anything we agree on that belongs in core and can be stable and
> 4. Are there plugin development guidelines?
> 5. How is the plugin system supposed to work?
The first stage is by simply adding a search path. We can make it
more sophisticated in time - i.e. plugins that can get loaded by
BioRuby core, etc. Some of it has already been done by us, but needs to
> More practically I have created a library for calculating the
> isoelectric point of a protein using Ruby
> Using shoulda as the testing framework. I would like to turn it to a
> bioruby plugin while adhering to a 'bioruby plugin development
> standard' if it exists.
Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module
naming conventions and name your project like bioruby-xxxx-plugin, so
it is clear it can work that way.
> Please advise
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