[Bioperl-l] bioperl-run executable

Jason Stajich jason at bioperl.org
Thu Oct 19 21:06:43 UTC 2006

It can be reset now but of course this not a very nice way of doing it:

$Bio::Tools::Run::Alignment::Clustalw::PROGRAM_NAME = 'clustalw_smp';

I am not sure if there are pros and cons to making it a getter- 
setter, but if you want to run with it, please do.

The whole run system has been hard to keep people adhering to a  
standard (and the standard has changed a bit) so some auditing is  


On Oct 19, 2006, at 11:47 AM, Nathan Haigh wrote:

> 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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Jason Stajich, PhD
Miller Research Fellow
University of California
Dept of Plant and Microbial Biology
321 Koshland Hall #3102
Berkeley, CA 94720-3102
lab: 510.642.8441

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