[Biojava-dev] Biojava and biomanycores

[forumjspro at gmail.com]

Thank you for the answers from Richard and Mark.
I will use ExecRunner in the next release.

Jean-Stephane

Le 21 oct. 09 à 23:20, Richard Holland a écrit :

> 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/
>