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

25 Jan 2016


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