Thanks for the detailed breakdown of the places to check, Carl! I was able
to fix the issue following the steps you've outlined. For the benefit of
other readers, here is what I did to fix it:

On Tue, Jan 26, 2016 at 10:09 AM, Carl Eberhard <>

> Hi, Oksana
> There are a few places to look and things to check in this situation.
> *First*, are other visualizations working on your production instance? Do
> you see the visualization icon/button and does the dropdown there have the
> 'charts' visualization on tabular files (like bed)?

Yes, I am able to see other visualizations.

> On the admin side for this, when your instance starts up you should see a
> section of logging data for visualizations that are loaded or error in the
> paster log. They're shown after the converter tools output logging info and
> before the job runners output theirs. They look something like:
> galaxy.web.base.pluginframework INFO 2016-01-26 09:57:37,989
> VisualizationsRegistry, loaded plugin: phyloviz
> You should see the standard visualizations load there including
> 'phyloviz'. If there's a problem, then you'll see a stack trace and a
> message saying that it was skipped.
Logs where showing no problems.

> *Second*, if visualizations are working well for other types, can you try
> uploading a phyloxml file and seeing if phyloviz will launch from that
> data? There's an example in this history:
Uploaded phyloxml sample and it was showing visualization icon.

> *Third*, it may be an issue with how the datatype is being referenced in
> the phyloviz config file (when compared with your datatypes_conf.xml file).
I've checked datatypes_conf.xml file and the lines that describe newick and
nexus datatypes where commented out. A bit silly, but that was what was
breaking it. Uncommenting them fixed the issue.

Thanks for all your help, guys!

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