[Bioperl-l] ...analysis interfaces

[Martin Senger]

> 
> Incidently, if those module names look really long and scary to you - I
> hope that the work that Martin is doing to build a general AnalysisFactory
> object will allow us to do (names subject to change of course)
> 
> my $factory = new Bio::Tools::Run::AnalysisFactory(-type => 'local');
> 
> my $protml = $factory->program('protml'); # or some other coding
> 
> $protml->parameter( .. );
> my ($rc,$results) = $protml->run();
> 
> AND substitute 'local' for 'ebi.ac.uk:novella', or 'pasteur.fr:pise' (or
> something more GRID-like) to run these analysis in their compute queues.
> Hence the need for fairly standard and simple interfaces to the
> applications and hiding of all the details in a result object IMHO.
>
   For those impatient, you can look at the interfaces I am proposing for
the AnalysisFactory and for the Analysis itself at 
http://industry.ebi.ac.uk/soaplab/Perl_Client.html. But keep in mind that 
the documentation still uses wrong namespace (it will be changed to 
Bio::Tools::Run::AnalysisFactory etc.).
   The interfaces are implemented now in order to access soap-based emboss 
server, but the idea is to use the same interfaces to access locally 
installed emboss, as well. Then it will be possible to do what Jason 
suggested above: -type => 'local', or -type => 'soap' etc. I will be 
working with Heikii to fit his emboss modules into this schema (if I can 
convince him :-)), and I hope that the same will be possible for 'Pise'.
   Martin

-- 
Martin Senger

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