Hi
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
result_type="datatype">data.Data< to result_type="datatype">interval.Interval
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