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 <h...@fmi.ch
<mailto: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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