I recently upgraded our local Galaxy instance from 21.09 to 22.05 and I noticed two things:
As recommended in the documentation, I switched from supervisor to systemd using the sample config file provided: however, when Galaxy is started this way, tools give errors such as:
jobs_directory/052/52678/galaxy_52678.sh: line 9: mkdir: command not found
as if the PATH was not right…
If I start Galaxy manually from the virtualenv using
galaxyctl start, no such error appears.
I had set up Galaxy reports on “/reports”, but could not find a way to start it again on a prefix in the new version. Gravity states it handles Galaxy Reports, but it does not with the (modified) sample config file, and if I start it using
run_reports.sh, it still only listens on “host:9001/”, not “host:9001/reports”. Setting
galaxy_url_prefixdoes not change anything.
Am I missing something?