[Biojava-l] Job launching system

[Brian Gilman]

Hello all,

	I'd be interested in this system as we have just put in a system
to do this into omnigene. If you go to our cvs repo you can find all the
SOAP classes and EJB's in edu.mit.wi.omnigene.webservice.analysis and
edu.mit.wi.omnigene.analysis. 


	I have a few questions though...Have you written a JNI layer that
interacts with LSF?? Or is this a command line program that does a
runtime.exec() ?? 

				Cheers,

					-B

-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On Mon, 27 May 2002, Schreiber, Mark wrote:

> Sounds interesting,
> 
> Is there overlap here with J2EE? Not entirely sure what you mean by
> batch queues but I assume it would be along the lines of submitting jobs
> to a blast farm or similar.
> 
> - Mark
> 
> > -----Original Message-----
> > From: Keith James [mailto:kdj@sanger.ac.uk] 
> > Sent: Saturday, 25 May 2002 5:38 a.m.
> > To: BioJava List
> > Subject: [Biojava-l] Job launching system
> > 
> > 
> > 
> > Just recently I've been working on a system for loading our 
> > batch queues in a trackable manner and I'm wondering whether 
> > there is any interest in adding it as a biojava cvs module. 
> > In some ways it's a bit like a simplified Ensembl pipeline 
> > minus all the application-specific bits (e.g. program output 
> > parsing) but with support for jobs being "owned" by more than 
> > one project. The idea was to decouple running programs from 
> > parsing output and storing the data.
> > 
> > All the resource management is of course delegated to a batch 
> > system like LSF or PBS, although without a batch system it 
> > can just run stuff on the local host. The DB persistence is a 
> > bit naive at the moment (it might need some caching).
> > 
> > Features:
> >  Job ownership
> >  Job dependencies (both && / || children) and retries on 
> > failure  Java native interface to LSF for submission/queue 
> > monitoring  Jobs implement standard Java MutableTreeNode 
> > interface (-> JTree GUIs)  Command line generation with 
> > Velocity Template Engine  Plugin job selection policies  
> > PostgreSQL and Oracle support  Logging with log4j  Email notifications
> > 
> > Anyway, let me know.
> > 
> > Keith
> > 
> > -- 
> > 
> > -= Keith James - kdj@sanger.ac.uk - 
> > http://www.sanger.ac.uk/Users/kdj =- Pathogen Sequencing 
> > Unit, Wellcome Trust Sanger Institute, Cambridge, UK 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
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