[Biojava-dev] Biojava and biomanycores

[Richard Holland]

BioJava does have a facility for launching local processes - check out  
this page:

    http://www.biojava.org/docs/api/org/biojava/utils/ExecRunner.html

All the BioJava code does is wrap Runtime in some nice programmer- 
friendly cotton wool. The best bit is the part that kills the process  
if it overruns a predetermined time limit (this has to be set  
explicitly - by default there is no time limit).

cheers,
Richard

On 21 Oct 2009, at 22:03, forumjspro at gmail.com wrote:

> Dear all,
>
> I'm one of the people who is trying to develop the biomanycores  
> project (www.biomanycores.org) which aims to give access to  
> efficient parallel algorithms developed for GPUs to bioinformaticians.
>
> To reach this goal we want to provide interfaces to those algorithms  
> through Bio* frameworks. People will have to change only some lines  
> in their Bio* code to use more efficient tools. In order to realize  
> such interfaces, it is necessary to launch the command line tool and  
> to retrieve results. I didn't see in the BioJava API a class  
> enabling to do such a thing although a mechanism seems to exist in  
> BioPython or BioPerl.
>
> I would like to know if I miss something in the API and, if it is  
> not the case, what could be the best way to launch external programs  
> to stay in the spirit of BioJava. For the moment, I use the trilead  
> package to launch commands on distant computers and the Runtime  
> class in the standard API to launch local commands. But may be it is  
> completely irrelevant to add such functionalities to BioJava.
>
> Please let me know what do you think about it.
>
> Best regards
>
> Jean-Stephane
>
> Jean-Stephane Varre
> http://www.lifl.fr/~varre
> http://www.lifl.fr/SEQUOIA
> http://bioinfo.lifl.fr
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/