Hi Peter, 

> Code looks interesting. This is for Univa Grid Engine?

In its current state its tailored for the Univa Grid Engine. But the drmaa 
library code that is based on job_info() and wait() should run on all grid 
engines. 
For the command line based code changes might be necessary for the different 
grid engines. (Currently there is only a small bug, because wait() is currently 
called twice for finished jobs: in the repeated polling and then in the final 
check. The second call won't work which causes a fallback to qacct. I will fix 
this 
soon.) 
I guess that the output of qstat and qacct will be different. But I think this 
can be configured one just needs a way to get the info which grid engine is 
running. 

> In terms of the upload jobs, are those not designed to be run as 'local' jobs 
> and not with the 'real user' setting?

Sounds reasonable, but this is not what is happening on my installation of 
galaxy. Any idea where I could start to find the problem. 

Best, 
Matthias
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