I just updated our Galaxy from 15.10 to 16.04. I also wanted to update the tools installed, but I'm (again) getting a whole bunch of different errors.
Some of the updated tools rely on package_cairo_1_12_14, which fails, because it cannot find some of it's dependencies (see package_cairo_errors.jpg):
> Error installing tool dependency fontconfig version 2.11.1: Unable to locate required tool shed repository named package_fontconfig_2_11_1 owned by iuc with revision 2ce32675340e.
> Error installing tool dependency freetype version 2.5.2: Unable to locate required tool shed repository named package_freetype_2_5_2 owned by iuc with revision 3b09e7916896.
In the main overview of the repository I also see the message "Dependency was not resolved by any resolver module." (see package_cairo_resolver.jpg). Is this related and something I should worry about? I did not touch the resolver configuration, I left
the line in galaxy.ini commented.
I also don't understand why it tries to install a different revision of a package repo that's already installed. I'm having similar errors for some other packages.
Furthermore, when I try to "Get Updates" for cuffdiff, I get an internal server error (see cuffdiff_update_error.txt). The same for macs2 (see macs2_update_error.jpg).
When I try to install the newest version of cuffdiff from the toolshed, after I click "Install to Galaxy", I get a "Request-URI
Too Large" error (from apache I guess). The last message before it fails in the Galaxy log is "Building repository dependency relationships...".
I'm a bit reluctant to update any package repositories I have installed, since in the past this lead to dependencies breaking. Also uninstalling and reinstalling usually
doesn't help, since the database keeps the records and once it's messed up it stays messed up. I checked on the galaxy-stable docker image and there everything works fine, so I guess it's related to my Galaxy instance, not the package/tool repositories.
Any help on how to solve this is greatly appreciated!
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