Upgrade to 22.05: "mkdir: command not found" and reports.yml


I recently upgraded our local Galaxy instance from 21.09 to 22.05 and I noticed two things:

  1. 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.

  2. 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_prefix does not change anything.

Am I missing something?

Hi @ppouchin

It is recommended to upgrade Galaxy in the order of releases. Did you first upgrade to 22.01, then 22.05? Releases — Galaxy Project 22.05.1 documentation

If not, the developers will likely ask for you to try that first. But let’s see if they have advice now. I posted your question to the Matrix admin chat. They may reply here or there, and feel free to join the chat. You're invited to talk on Matrix

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