This gets tricky, can you check if the visualisations are loacted under this path and do double-check the filetypes? The icon is only displayed with the correct datatype.
Am 25.01.2016 um 17:37 schrieb Oksana Korol: > It's un-commented in both local and production. Still there is no icon > in production. > > Cheers, > Oksana > > On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning > <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote: > > Hi, > > can you please check this setting? > > > https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L270 > > 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.gruen...@gmail.com > <mailto:bjoern.gruen...@gmail.com> > > <mailto:bjoern.gruen...@gmail.com > <mailto:bjoern.gruen...@gmail.com>>> > > To: Oksana Korol <oko...@gmail.com <mailto:oko...@gmail.com> > <mailto:oko...@gmail.com <mailto:oko...@gmail.com>>>, > > galaxy-dev@lists.galaxyproject.org > <mailto:galaxy-dev@lists.galaxyproject.org> > > <mailto:galaxy-dev@lists.galaxyproject.org > <mailto:galaxy-dev@lists.galaxyproject.org>> > > Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on > CentOS > > Message-ID: <56a3ccb3.9020...@gmail.com > <mailto:56a3ccb3.9020...@gmail.com> > > <mailto:56a3ccb3.9020...@gmail.com > <mailto:56a3ccb3.9020...@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 > > > -- > ___________________________________________________________ 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/
