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 <carlfeberh...@gmail.com> wrote: > 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: > > https://test.galaxyproject.org/u/carleberhard/h/phyloviz > 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! Cheers, Oksana
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