[Bioperl-l] bioperl-run executable

Nathan Haigh N.Haigh at sheffield.ac.uk
Thu Oct 19 14:47:01 EDT 2006


Quoting Chris Fields <cjfields at uiuc.edu>:

> I think a lot of the bioperl-run modules use Bio::Tools::Run::WrapperBase
> but I'm not sure.  I haven't used them very much myself but plan on making
> wrappers at some point soon for some programs I use.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign 
> 

On closer inspection of a couple of other modules (Clustalw.pm and TCoffee.pm), they seem to hardcode the exe name in $PROGRAM_NAME and have a sub
(program_name) that simply returns this value. I'd like to see the program_name become a getter/setter so users can change the default and have the
string stored in the factory object.

Does it matter that Bio::Tools::Run::WrapperBase is in bioperl-core not bioperl-run? I suppose not since bioperl-core is a prerep for bioperl-run but
wouldn't it make sence to go in bioperl-run?

Nath


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