Glad to hear it is working now, Mike!
I don't think having both files hurts, but creating an extra file when you don't need to is certainly a wasted effort. Having the instruction clarify this makes sense.
This is good feedback - thanks for taking the time to let us know how it works from the user's side. I'll make sure that Jeremy (our Trackster author) sees this.
Take care,
Jen Galaxy team
On 3/19/13 7:20 AM, Michael Axtell wrote:
Hi Jen, thanks for your reply.
Yes, this is a visualization on Public-Main.
Just tried it this morning, without also loading the .len file, and it works. Not sure whether the server errors yesterday were from the presence of both the .fasta and .len file, or some internal server that was resolved after the last time the main instance was updated .. but either way no problems now. Thanks!
Maybe one small suggestion .. the way the 'custom build' dialog is set up currently doesn't explicitly say that EITHER a fasta OR a .len file is required. I had assumed that BOTH were required since there were forms for both and no explicit statement about it. Perhaps a small statement to let users know that only one or the other is required, and that with .len you won't get the bases.
Cheers, Mike
On Tue, Mar 19, 2013 at 2:41 AM, Jennifer Jackson jen@bx.psu.edu wrote:
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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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