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 <h...@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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