Hi Jeremy,
Thanks for you assistance. I would love to try your suggestions, but
Galaxy won't start anymore.
I have found the root cause of the problems: my home partition has
become too small, due to a fat 'job_working_directory'. I didn't expect
it to become so big (especially with tophat
Hi Joachim,
It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for
1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2)
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
I've seen this once or twice before but haven't been able to track down the
issue yet.
Here are two workaround that may help you out:
(1) Add the dataset to a
Thanks for your suggestion, Hans-Rudolf. Unfortunately, no success.
Looking into it bit deeper. Keep suggestions coming ;-)
Joachim
On 11/08/2012 05:00 PM, Hans-Rudolf Hotz wrote:
Hi Joachim
This might be completely unrelated, but your situation reminds me of
our case when we did the last
Can you please verify that you're running the most recent dist?
In the most recent dist, requireJS modules are used, so Dataset is prefixed
with its module, e.g.
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Nearly all saved viz's just show a blank main window, while just
displaying the Galaxy header and the trackster header bar.
In contrast, one visualisation gives this error:
ConverterDependencyException: 'A
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that you're
seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Clearing cache did not solve it.
The Js console reports (when trying to visualize an short-read alignment):
Uncaught ReferenceError: Dataset is not defined visualization.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Uncaught ReferenceError: Dataset is not defined
Hi Joachim
This might be completely unrelated, but your situation reminds me of our
case when we did the last update (to Oct 5th release):
All previously stored visualizations didn't work any more a first. I had
to modify the datatypes_conf.xml file by adding
the following line:
datatype
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