Dear Galaxy Users,
Forgive me in advance, but I am a VERY new Galaxy user!
I am trying to go through the Galaxy 101 tutorial provided on the
galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101). The
first step asks to get exon data of Chromosome 22 from UCSC database,
and the second step asks to get the SNP data from the same database.
When I do these two steps, I understand the history items should turn
green once they are processed, however after a few hours these items
remain grey. Am I doing something wrong?
Any help would be greatly appreciated!
Thank you in advance,
If you are using one of the public Galaxy servers (e.g.
http://main.g2.bx.psu.edu/), then it's quite probable that there a
jobs queued in the system by other users. If your history item is grey
that means the job has been successfully submitted and is waiting its
in the queueing system. When the system is busy it will take longer
the jobs to be submitted due to the high demand.
In short - give it some time, it will run eventually.
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601
Graham is correct in stating that a "grey dataset" indicates that the
job is still in the queue waiting to run. When the public server is
busy, this delay can vary based on a few factors, but a UCSC Table
Browser data extraction is not a job that would be expected to take
That said, the public server was known to be slower later yesterday
through this morning. We are actively working to resolve this and you
should notice improvement shortly.
I was able to get a small test job through (also a UCSC Table data
extraction) even during this time - with some delay, but not on the
order of several hours. Have your jobs completed now and were you able
to work through the exercise since first reporting the issue? If jobs
were stalled, please try again one more time and if there is problem
that continues through this afternoon, please let us know. The
was designed to not be computationally intensive - and you should be
able to complete it during a single work session.
Just to let you know, sometimes it appears that jobs are waiting, when
actually all that is needed is a "History refresh" to update the panel
to show the current status. I've misinterpreted status myself by
forgetting to do this on occasion (still!). A manual refresh certainly
isn't always needed, but is worth knowing about. There is a small
double-arrow rounded icon at the top of the History panel, to the left
of the gear icon, that you can click to do the refresh, here is a
picture of it:
Hopefully this helps,
Galaxy Support and Training