Hi Carl
What was the datatype (listed as 'format') of the dataset you tested with here?:
However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize")
any data type, eg wig, tabular, bed, etc I currently have: 'result_type="datatype">data.Data' in ~/config/plugins/visualizations/trackster/config/trackster.xml If I change that to 'result_type="datatype">interval.Interval' (and do a restart), I lose the bar-plot icon for wig and tabular. It is still there for the bed file in the history.
Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype?
They never show up, I don't get the menu when I click on the bar-plot icon (for bed and/or interval data typ). It goes straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. Hans-Rudolf
Thanks for the report and any info you can provide, Carl
On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
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 _____________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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