Setting up visualization on Galaxy on CentOS
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
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>
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participants (2)
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Björn Grüning -
Oksana Korol