[GE users] Illumina/Solexa pipeline on large SGE 6.2 systems?

Chris Dagdigian dag at sonsorol.org
Fri Sep 5 21:02:10 BST 2008


Thanks Sean!

Nice find, I found the 'distmake on SGE' page here:

http://distmake.sourceforge.net/pmwiki/pmwiki.php?n=Main.SGEIntegration

Are there any writeups around that summarize what benefits or what  
problems are avoided when going from qmake to distmake?

On our end we've been using a qmake wrapper script that looks like  
this for the Illumina pipeline:

> #!/bin/sh
>
> #$ -cwd
> #$ -v PATH
> #
> ## We use this with the Illumina pipeline to distribute
> ## the make commands across the SGE grid rather than deal
> ## with the standard non-distributed Unix make program.
> ##
>
> qmake -cwd -v PATH -inherit -- recursive
>


... no SGE issues so far with this but I suspect our instrument data  
and cluster sizes may be smaller than the others posting on this topic.

-Chris



On Sep 5, 2008, at 3:55 PM, Sean Davis wrote:

>
> I should have mentioned that when we have use SGE for the pipeline, we
> have not been using qmake, generally, but distmake, which is SGE
> aware.
>
> Sean


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