Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

25 Jan 2016


      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.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>> wrote:
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>
    >     <mailto:bjoern.gruening@gmail.com
    <mailto:bjoern.gruening@gmail.com>>>
    >     To: Oksana Korol <okorol@gmail.com <mailto:okorol@gmail.com>
    <mailto:okorol@gmail.com <mailto:okorol@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: <56A3CCB3.9020503@gmail.com <mailto:56A3CCB3.9020503@gmail.com>
    >     <mailto: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
    >     > --