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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/