(oops, to continue the truncated sentence in the prev. email):
You can change that by editing the ...
config/trackster.xml 'datatype' as you did in your email to restrict what
Trackster can run on.
(sorry about that)
On Wed, Aug 27, 2014 at 9:39 AM, Carl Eberhard <carlfeberh...@gmail.com>
wrote:
> 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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>>
>
>
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