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
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland