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