On Aug 25, 2012, at 10:07 PM, Kenneth R. Auerbach wrote: Hi Kenneth, If you haven't taken some of the steps like using PostgreSQL instead of SQLite, and setting 'set_metadata_externally = True', please do so, as these will make a big difference on performance. Full documentation is at: http://usegalaxy.org/production/ You can't restart the server and recover running jobs if they're running through the local runner. Jobs that are waiting to run when the server shuts down will not be lost. To recover running jobs, you'll need to set up one of the cluster job runners (which you can do, even if you're only submitting jobs to the local system). --nate