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 extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>


and add
<converter file="bed_to_fli_converter.xml" target_datatype="fli"/>

and <converter file="gff_to_fli_converter.xml" target_datatype="fli"/>

to the bed and gff definitions, respectively.

(the differences are easy to spot when you compare your 'datatypes_conf.xml' file with the new 'datatypes_conf.xml.sample' file.)


After making the changes and restarting the server, the saved visualization were re-indexed as soon as I tried to open them, but finally, the were visible again.


Regards, Hans-Rudolf


On 11/08/2012 04:21 PM, Joachim Jacob wrote:
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     tracks.js:1


Thanks,
Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 11/08/2012 04:14 PM, Jeremy Goecks wrote:
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.

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 dependency (bgzip) was in an error
state.'

Any help appreciated, thanks.

Joachim

--
Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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