Is the main usegalaxy server running, or is it just under a high work load? I've run cufflinks, and out of 12 files, 2 files had failed cufflinks the first time for unknown reasons:
This job failed for reasons that could not be determined. Please click the bug icon to report this problem if you need help.
Since the other 10 files worked fine, I re-ran cufflinks and the jobs were highlighted yellow, and remained yellow for 8 hours. I ended up permanently deleting the files, thinking that perhaps the process froze.. and ran them once again. These jobs now have been highlighted grey with an exclamation mark for the past 14 hours, and haven't even started running. Is the server working properly? At this point, I am regretting permanently deleting the running files, but even so, 8 hours of "yellow," and 15 hours of "grey" seem way too long for cufflinks?