Hello Mike,

This is a visualization using a custom reference genome? On the public Main Galaxy instance at https://main.g2.bx.psu.edu/ (usegalaxy.org)?


First, you won't need both a .fasta dataset and a .len file - just a .fasta dataset would be fine (preferred actually, since then you will have the genome bases in the vis). The .len option is for when a .fasta dataset is not available.

If you haven't done so already (at a time after about 3pm US East coast time, when the Main instance was last updated), please try to build another visualization, using just the fasta dataset as the custom genome. Be sure to double check .fasta format, this wiki can help:
http://wiki.galaxyproject.org/Learn/CustomGenomes
(be sure to see section #7: Troubleshooting)

Then, you are still having problems, a shared history would be the best way to find out what the problem is. Under the History panel, top right corner, there is a gear icon - click on that to open a pull-down menu. Choose "Share or Publish", generate a share link (first button), and copy/paste that into a a reply email (to just me, not list, to preserve your data privacy). Please include the steps you followed to produce the error so that I can attempt to reproduce.

Hopefully this is cleared up by now, but if not, we can find out what the issue is and get it resolved,

Jen
Galaxy team

On 3/18/13 10:43 AM, Michael Axtell wrote:
Hello,

My attempts to build a new custom genome failed on the public server
today, with a server error ..
"Server Error

An error occurred. See the error logs for more information. (Turn
debug on to display exception reports here)"

I checked md5 of the fasta file which I was building and it was fine,
pretty sure the .len file was OK too.  No job ever starts .. server
error is returned very quickly.

Any advice would be appreciated, thanks in advance.

- Mike


--
Michael J. Axtell, Ph.D.
Associate Professor
Dept. of Biology
Penn State University
http://axtell-lab-psu.weebly.com
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at usegalaxy.org.  Please keep all replies on the list by
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