CC'ing the galaxy-user list because I am assuming that your question is about the free public server ("Main") @ usegalaxy.org / main.g2.bx.psu.edu. If you have any future questions about Main, please post them to Galaxy-User so that others can see the question and respond.
If I am reading the qstat output correctly, there are currently ~140+ jobs in the NGS queue, which means that Main is currently under very heavy load. The best thing to do is let the jobs sit in the queue. Killing and restarting them bumps them to the end of the queue.
We are currently discussing a number of options for letting users know in situations like this, that while the job is not currently running, it is in the queue, and is moving forward.
PS: and the number of jobs in the queue has dropped by 2 since I started typing this email.
On Fri, Nov 30, 2012 at 10:05 AM, Lewis Bowman email@example.com:
I have tried repeatedly to run Cuffdiff using cuffmerge output (38) and cufflinks output (25 and 29). In every case the job does not begin to run and status says"Job is waiting to run." Has Galaxy been down for the last several days? I am unsure what to do since I have received no error message. Thanks for you help.
-- Lewis H. Bowman Department of Biological Sciences University of South Carolina Columbia, SC 29208 PH: 803-777-5157 FAX: 803-777-4002 EMAIL: firstname.lastname@example.org