On Jan 5, 2012, at 11:29 AM, Ryan Golhar wrote:

> On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:
> 
> > On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar <ngsbioinformat...@gmail.com> 
> > wrote:
> > I'm adding Data Libraries to my local galaxy instance.  I'm doing this by 
> > importing directories that contain bam and bai files.  I see the bam/bai 
> > files get added on the admin page and the Message is "This job is running". 
> >  qstat shows the job run and complete.  I checked my runner0.log and it 
> > registers the PBS job completed successfully.  But the web page never 
> > updates.  I tried to refresh the page by navigating away from it then back 
> > to it, but it still reads "This job is running".  How do I fix this?
> >
> > Some more information...I check my head node and I see samtools is running 
> > there.  Its running 'samtools index'.  So two problems:
> >
> > 1)  samtools is not using the cluster.  I assume this is a configuration 
> > setting somewhere.
> 
> See set_metadata_externally in universe_wsgi.ini.  This should be set to True 
> to run on the cluster.
> 
> If you haven't seen the rest of the production server documentation, see 
> http://usegalaxy.org/production
> 
> 
> This is already set.  I set this in universe_wsgi.ini (and 
> universe_wsgi.webapp.ini and universe_wsgi.running.ini since I'm using a 
> proxy server and load balancer on Apache).  This was one of the first things 
> I set up.

Does the upload tool run on the cluster?  See upload1 under 
[galaxy:tool_runners] in universe_wsgi.runner.ini.

--nate


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