I set it to run on the cluster:

[galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini 
#upload1 = local:///


On Thu, Jan 5, 2012 at 11:33 AM, Nate Coraor <nate@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 <ngsbioinformatics@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