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 <j...@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
___________________________________________________________
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org





--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___________________________________________________________
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
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 http://lists.bx.psu.edu/listinfo/galaxy-dev

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