[Bioperl-l] new cvs module bioperl-runnable

[Heikki Lehvaslaiho]

Separating the modules to an other cvs module might help manging the large 
number of modules 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. How about using the Registry to centrally manage the 
names of the binaries? We have not really started using Registry even for 
databases!



Catherine Letondal wrote:

> 
> Pise indeed not only brings 276 files but 3.8 Mo more in bioperl-live.
> I have of course thought about having fewer files, for instance not to have one
> file for each program in Bio/Tools/Run/PiseApplication. How is it actually for
> EMBOSSApplication? You need at least the informations from the ACD file
> to be somewhere I guess? 



Cathrine,

EMBOSS wrapper has only three modules:

Bio::Factory::EMBOSS
Bio::Tools::Run::EMBOSSApplication
Bio::Tools::Run::EMBOSSacd

Factory knows about possible application names and can create an application 
given the name. Application can call for an ACD object which gets populated 
with correct data. At the moment Data::Dumper is used to print the ACD 
informaton out , but that is easy to change inot some kind of prettier 
formatter if needed.

In similar vain you could device a standardised description format for Pise 
(a la ACD) which can be retrieved over the net. Should save you a lot of 
trouble updating just in one place, instead in server and in all the clients.

	-Heikki


> Regarding PiseApplication/program.pm files, there is really useful stuff in them:
> all the information about each parameters, and the documentation about them (so that
> you can do a perldoc Bio::Tools::Run::PiseApplication::program). Hence the 3.8 Mo. It could
> be reduced maybe by removing information that is only needed on the server or in HTML
> forms.
> 
> I think the idea of having a separate bioperl-run for people not needing to run
> analyses is a good one though. 
> 
> 
>>The whole extra effort of writing stuff in Bio::Tools::Run from our side
>>was because we wanted to make sure people could use our work for
>>standalone analyses, so I wouldn't like to see them move to
>>bioperl-pipeline. I like the bioperl-run CVS module idea, that is a nice
>>split. Basically it's important for people to realise that the pipeline is
>>workflow management code, and not much else, and it wraps whatever
>>databases and run modules one wants to wrap.
>>
>>Another side comment is about the Pise run modules. This is in no way a
>>criticism, there is lots of useful code, but I wonder if we have just
>>"overlapped it" with bioperl run, and whether some reationalisation should
>>be done (i.e. what is covered by Pise, what is covered by
>>Bio::Tools::Run) 
> 
> 
> If Bio::Tools::Run is intended to contain API for running programs (local or remote), 
> there is no real difference, they cover the same need.
> There is a nice Bio::Tools::Genscan module, but where is the Bio::Tools::Run::Genscan?
> Here: Bio::Tools::Run::PiseApplication::genscan.
> There is a Bio::Tools::Grail module ... and the Bio::Tools::Run::PiseApplication::grailclnt.
> There is no Bio::Tools::Toppred yet (but one is ready in
> ftp://ftp.pasteur.fr/pub/GenSoft/unix/protein/toppred/ see ToppredXML.tar.gz ) - again it
> could be combined with Bio::Tools::Run::PiseApplication::toppred. Etc...
> 
> So these modules enable people not only to run programs without having to install 
> them locally, but also just to use available bioperl parsers within a single script.
> 
> Another benefit is the programming time for an additional program: depending on the
> number of parameters, adding a new program in Pise takes from a few minutes to a few 
> hours.
> 
> However, the main question remains: is bioperl the place to have code to run 
> bioinformatics programs? :-)
> 
> --
> Catherine Letondal -- Pasteur Institute Computing Center
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-- 
______ _/      _/_____________________________________________________
       _/      _/                      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
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