Hi, Hans,

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")

Trackster by default accepts all datatypes (all subclasses inheriting data.Data) and is the only visualization that ships with Galaxy that allows visualization on all datatypes. You can change that by editing the

'Charts' and 'scatterplot' can work with any tabular datatype (or subclasses of). If a datatype isn't tabular, those visualizations won't appear as options in the menu.

Do the 'charts' and 'scatterplot' visualizations show up in the visualization icon popup menu when you check on an interval or bed datatype?

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> 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
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