Hi,
Recently we’ve been playing around with deploying Galaxy on our Kubernetes environment - which we now have been able to successfully do so. Running regular tools & containerized tools up to our preference was achieved. The last step is to also include the Interactive Tools in there - specifically Jupyter Notebook.
The documentation on this topic with respect to Kubernetes is rather limited, nevertheless I’ve used the following guides:
- https://f1000research.com/slides/10-833
- Galaxy InteractiveTools — Galaxy Project 24.2.dev0 documentation
However, I’m running into issues and I hope that someone can help me. The error message in the interface is “Kubernetes failed to export tool ports as services”. When trying to dive into that, I noticed that a service for Jupyter Notebook is being created - but it fails to find it’s corresponding galaxy pod. "error: error from server (NotFound): pods “gxy-my-galaxy-release-48” not found in namespace “kni-galaxy2”. Side note: All Galaxy job pods end with a random string - whereas this service is looking for an incremental value…?
When I subsequently disable the <entry_points>*</entry_points> block from the Jupyter XML I can see that the Jupyter service is not being created (as expected) - but the galaxy pod (which was previously missing) is being created. Obviously, without the corresponding service there is no communication between the two.
So I’m a bit lost… anyone that can help?
values.yaml
interactivetool_jupyter_notebook.xml
The initial error comes from: galaxy/lib/galaxy/jobs/runners/kubernetes.py at dev · galaxyproject/galaxy · GitHub (__configure_port_routing)
