[Bioperl-pipeline] Re: runnable_parameter and analysis_parameter

[shawnh@fugu-sg.org]

Runnable parameters are parameters passed to the runnable module
while analysis parameters are the ones passed to the wrapper.
The latter are geared more towards the acutally binary parameters
while the former are more for certain configurations like outputdir, workingdir
etc

It is differentiated to hopefully avoid confusion. 
I probably omitted the change for genscan.

shawn

On Mon, 6 Jan 2003, Xiao Juguang wrote:

> Hi all, Happy New Year!
> 
> Shawn, you have add the new tag of runnable_parameter and 'analysis_parameter', binary program parameters in xml and code, while removing the 'parameter'. But I do not understand so much the difference between them and how to use them. Now I am setting up a pipeilne for genscan with ensembl db. However, the problem is the Bio::Pipeline::Runnable::Genscan is not accordingly updated, it still use $analysis->parameter and now should be changed to something else, right? I changed it to $analysis->analysis_parameters, and it works, but i am not sure on the result.
> 
> Can you explain  the difference between them and how to use them? Thanks
> 
> Juguang
> 
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
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