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)? 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. *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 *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). Can you check the datatypes api on your production instance: $YOUR_ROOT/api/datatypes/mapping ...and search for the 'nhx' datatype? You should see something like towards the bottom of the response: "nhx": "galaxy.datatypes.data.Newick", I believe, this last part of this *should* match the line in phyloviz's config file: <test type="isinstance" test_attr="datatype" result_type="datatype"> data.Newick</test> Thanks, Carl On Mon, Jan 25, 2016 at 1:37 PM, Oksana Korol <oko...@gmail.com> wrote: > It get even trickier... I just double-checked my local install, and I > didn't have visualization_plugins_directory uncommented, and yet, it works > on local install.... > > >This gets tricky, can you check if the visualisations are loacted under > >this path > > If you mean phyoviz and other plugin code from github, then yes, it's > there. I doulbe-checked the files and permissions as well, just to be sure. > > > and do double-check the filetypes? The icon is only displayed > > with the correct datatype. > > I did... I use exactly the same newick tree file for local and for > production test. Upload it, selecting nhx as a datatype. Double-check the > datatype by clicking on a pencil icon - it's nhx on both, but it works on > local and doesn't on production. > > I'll keep digging and comparing the two installs. If you think of anything > else, let me know. > > Thanks! > > Oksana > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
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