Hi, can you please check this setting? https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L2... Thanks, Bjoern Am 25.01.2016 um 15:46 schrieb Oksana Korol:

Thanks, Bjoern!

For my local install of Galaxy, logging in as a user worked and the icon is showing up (although I still had to manually go and change permissions on all the mako templates in ./database/compiled_templates directory). But our production instance of Galaxy (also v15.07 on CentOS 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged in as a user. In production, it is not a clean install, but an upgrade from previous versions, so it is harder to figure out what's going on. There are no errors in the logs, so I'm still looking for any kind of clues of what could have gone wrong with the visualization.

Cheers, Oksana

Message: 1 Date: Sat, 23 Jan 2016 19:55:47 +0100 From: Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> To: Oksana Korol <okorol@gmail.com <mailto:okorol@gmail.com>>, galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS Message-ID: <56A3CCB3.9020503@gmail.com <mailto:56A3CCB3.9020503@gmail.com>> Content-Type: text/plain; charset=utf-8

Hi Oksana,

this work for me in 16.01 (upcoming). Please make sure you are logged into your Galaxy as some user, not anonymous and than the Phyloviz Visualisation will be available from the small chart-symbol next to the (i) symbol.

Hope this helps, Bjoern

Am 22.01.2016 um 23:53 schrieb Oksana Korol: > Hi, > > I'm having trouble getting visualization icons, like Phyloviz, to show > up on my Galaxy instance running in CentOS 6.7. Here are the steps I > took, expecting it to work: > > 1. cloned Galaxy tag v15.07 (that's the version we need to run in > production) > > 2. Followed the steps in https://wiki.galaxyproject.org/VisualizationSetup > - Renamed datatypes_conf.xml.sample to > datatypes_conf.xml > - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit > - Installed BED Tools > - Added above tools to my user path (galaxy_utils dir is where > wigToBigWig and others are): > /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin > * > 3. Started Galaxy. > > 4. Uploaded a newick tree file (nhx), which is known to be displayable > in phyloviz on a Ubuntu instance of Galaxy > > 5. Made sure the datatype is nhx > > 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand > the file in history, but there is nothing there. > > At this point I don't know where to dig to find how I can fix it. Any > feedback, including your own stories for visualization setup or how I > can debug what's not being picked up where, would be greatly appreciated. > > Cheers, > Oksana > -- > :: > Oksana Korol > dataquarry.blogspot.ca <http://dataquarry.blogspot.ca> <http://dataquarry.blogspot.ca> > > > ___________________________________________________________ > 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/ >

___________________________________________________________ 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/