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!
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
T +352 46 66 44 5360