On Mon, Feb 20, 2012 at 8:08 AM, Bram Slabbinck <br...@psb.vib-ugent.be> wrote:
> Hi Dannon,
> If I may further elaborate on this issue, I would like to mention that this
> kind of functionality is also supported by the Sun Grid Engine in the form
> of 'array jobs'. With this functionality you can execute a job multiple
> times in an independent way, only differing for instance in the parameter
> settings. From your description below, it seems similar to the Galaxy
> parallelism tag. Is there or do you foresee any implementation of this SGE
> functionality through the drmaa interface in Galaxy? If not, is there
> anybody who has achieved this through some custom coding? We
> would be highly interested in this.
> thanks
> Bram

I was wondering about why Galaxy submits N separate jobs to SGE
after splitting (identical bar their working directory). I'm not sure if
all the other cluster back ends supported can do this, but basic
dependencies is possible using SGE. That means the cluster could
take care of scheduling the split jobs, the N processing jobs, and
the final merge job (i.e. three stages where for example it won't
do the merge till all the N processing jobs are finished).

My hunch is Galaxy is doing a lot of this 'housekeeping' internally
in order to remain flexible regarding the cluster back end.

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