[Bioperl-l] new cvs module bioperl-runnable

[Heikki Lehvaslaiho]

Catherine Letondal wrote:
> Heikki Lehvaslaiho wrote:
> 
>>Separating the modules to an other cvs module might help manging the large 
>>number of modules
> 
> 
> yes, definitely
> 
> 
>>but it does not help the main problem: how to oganize the 
>>wrappers and make sure that users are not confused by modules when binaries 
>>are not available.
> 
> 
> Since they are run on a remote server, they don't have to be available locally?
> I agree that whether the API is for local or remote execution
> should be more explicit in the bioperl hierarchy.
> Maybe Bio::Tools::Run::Local and Bio::Tools::Run::Remote distinction could be
> useful? Or, on the contrary should it be hidden to the user of bioperl?

The way I've been thinking it to be is that a wrapper has a default location 
   but when possible user coud change that. This has not been an issue so 
far but but I did wrote method Bio::Factory::EMBOSS::location() which can 
get two values 'local' and 'novella'. This method should ideally be in 
Bio::Factory::FactoryI and instantieated by all factories. NAme of the 
methods is , as always, open to discussion.


>>How about using the Registry to centrally manage the 
>>names of the binaries? We have not really started using Registry even for 
>>databases!
>>
> 
> 
> A registry would tell where to find the program, I guess?
> But again, you don't have to take care of this in using a client. It's the
> server's responsibility. In the perl code you just have to do:
> 	 my $program = $factory->program('genscan');
> What is currently done (for now!) in Pise factory, is to give a default
> location for the server of a program.

The way  you've set up Pise is fine for the time being. I just trying to 
come up with something general for managing local setup of programs that 
would make it easier to configure large number of binary wrappers.

	-heikki


> --
> Catherine Letondal -- Pasteur Institute Computing Center
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l


-- 
______ _/      _/_____________________________________________________
       _/      _/                      http://www.ebi.ac.uk/mutations/
      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________