Hello Jacob, Thanks for your help solving restart problem http://dev.list.galaxyproject.org/Cann-t-restart-server-after-updating-to... I am facing the same problem again but this time when running ./run.sh I get the following error: socket.error: [Errno 98] Address already in use galaxy.jobs.handler INFO 2013-07-18 03:28:46,328 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-07-18 03:28:46,328 job handler queue stopped galaxy.jobs.runners INFO 2013-07-18 03:28:46,328 LWRRunner: Sending stop signal to monitor thread galaxy.jobs.runners INFO 2013-07-18 03:28:46,328 LWRRunner: Sending stop signal to 3 worker threads galaxy.jobs.runners INFO 2013-07-18 03:28:46,328 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2013-07-18 03:28:46,329 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-07-18 03:28:46,329 job handler stop queue stopped Exception in thread JobHandlerQueue.monitor_thread (most likely raised during interpreter shutdown): Do you know how to solve the problem? Thanks Karen