As part of my upgrade/testing work, I am looking at the visualization plugins.

In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine.

All I have done was:

 - I defined the visualization_plugins_directory in the
   universe_wsgi.ini file

If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot

Next, I have tried it on our development server (after I have upgraded from "release_2014.04.14" to "latest_2014.08.11"). I changed the universe_wsgi.ini file.

I the logs I get:

galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/circster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/sweepster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster

wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me.

However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize"), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'.

On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/visualizations/trackster/config/trackster.xml I see the effects, ie if I change


I can restrict the visualization to only the interval data.

Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ?

Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation

Thank you very much for any hints and help



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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