[BioRuby] Guidelines for writing bioruby plugins

[George Githinji]

Hi Pjotr
Thank you very much for the explanation.

On Sat, Oct 9, 2010 at 12:05 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Hi George,
>
> 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
>> http://github.com/helios/bioruby-plugin-graphics
>>
>> 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
> maintained.
>
>> 4. Are there plugin development guidelines?
>
> Planned
>
>> 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
> solidify.
>
>> More practically I have created a library for calculating the
>> isoelectric point of a protein using Ruby
>> (http://github.com/georgeG/isoelectric_point_4_R).
>> 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
>
> Pj.
>



-- 
---------------
Sincerely
George
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/