[Bioperl-l] RE: remote blast job queuing

[Steve Chervitz]

Jason wrote:

>Happy to see your plan here - I sort of imagined the writing of report
to
>be done with a write_report() method in the Bio::SearchIO implementations
>just like we have a write_seq() method in SeqIO.  So blast.pm,blastxml.pm,
>fasta.pm etc could provide their own implementation of outputing a data
>stream.  Fine for there to be a Writer helper class but I am hoping we
can
>make bioperl as intuitive as possible and if all our IO systems can
>function in similar ways it makes learning the objects much easier.  Just
>a thought but feel free to convince me otherwise.

I have in fact added a write_report() method to SearchIO, and it works by
delegating to a Writer object that the user can specify and if not, a default
writer is used. It's pretty straightforward, I'll point you at some examples
when I get things checked in.

>> Another thing that's not in Jason's or my Bio::Search:: stuff is any
sort
>> of functionality related to running new search jobs. As Ewan mentioned
>before
>> (http://bioperl.org/pipermail/bioperl-l/2001-July/006020.html), it would
>> be good to tie into a novella-like system. (I believe Martin mentioned
>to
>> me the possibility of contributing novella to Bioperl. Don't know what
>the
>> current thinking here is).
>>
>> Steve
>
>I'd like to propose keeping anything that runs a job in the Tools::Run
>directory if possible - these would pass back a Bio::SearchIO stream in
>much the same way the current running of search tools works in that
>directory should work (Run::StandAloneBlast returns a BPlite or
>Tools::Blast object).

We're thinking along the same lines here. 

Steve

>What I think we need to do is flesh out the Factory::ApplicationFactoryI
>that Heikki started for EMBOSS and then provide a specific factory for
the
>apps we are interested in.  All the current ways one can run blast
>Tools::Run::StandAloneBlast and Tools::Run::RemoteBlast can comply with
>this interface.  Additionally the implementation of Pise and Novella
>clients for remote analysis and EMBOSS clients for local analysis (remote
>EMBOSS would be mediated through one of the remote clients likely).
>
>It would make sense (in my mind) to try and have all the implementations
>for running apps in common namespace.  My hope is that some of the hard
>work in defining the necessary interfaces that has been done with Pise
and
>BSA/NOVELLA could be used to build the interfaces in bioperl.
>
>So some work to unify these things - but would be great to have an
>interchangeable system for analysis programs and compute queues with the
>concept of the data object, the parser, and the analysis data stream
>all decoupled much the same way we have done for sequence objects,
>parsers, and databases.
>
>Maybe I am thinking too big here?
>
>-jason
>-- 
>Jason Stajich
>Duke University
>jason@cgt.mc.duke.edu
>
>