Hi Crystal, The galaxy-user@galaxy.bx.psu.edu mailing list would be the best for this question. All lists are described here: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists http://wiki.g2.bx.psu.edu/Mailing%20Lists Grey jobs are scheduled to run the and aere in the queue. While they are waiting to run, it is important to not start and restart, as this effectively movest them to the end of the line@ Hopefully this helps, Jen Galaxy team On 7/26/12 8:57 AM, Crystal Marconett wrote:

Hello,

I am trying desperately to get an answer to a question. I've been over the help area for an hour trying to find an email address to ask questions to, and the only one is the tophat people's email... which is not helpful, because the problem is starting the tool in Galaxy, not getting TopHat errors yet because the job is simply stuck on grey (waiting......)

The question: I am trying to start running tophat on my history in the Galaxy main wed interface. I started the job last night at 10pm. It's now 9am. The job is still "waiting to run", ie. grey. How long does it take the Tophat web interface to start? is there a data limit that above which Tophat can no longer run? I don't think this is right, I've run TopHat before on Galaxy with the Illumina whole body tissue data and it took a while, but not this long....

My username is: cmarcone@usc.edu the History's name is: Per-RNAseq The job is : #32, 33, 34, 35 (all grey Tophat for Illumina). The history has 65.7GB in it, and says it is using 21% (I assume the amount of allocated space left on the server).

Please help! And if this is not the right e-mail address can you forward this along to the correct one, please!!! or at least let me know the correct email to mail this too. Thanks! C

-- Jennifer Jackson http://galaxyproject.org