On Jan 5, 2012, at 11:41 AM, Ryan Golhar wrote:

> I set it to run on the cluster:
> 
> [galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini 
> #upload1 = local:///

Could you set use_heartbeat = True in the runner's config file and then check 
the resulting heartbeat log files created in the root directory to get a stack 
trace to the call of samtools?

Thanks,
--nate

> 
> 
> On Thu, Jan 5, 2012 at 11:33 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> 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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