Jupyter notebook does not work

[sveinugu]

I sent a bug report using the Galaxy bug reporting feature with all the details. I don't know who gets those reports, so task 1 is to locate the details! :)

[kjetilkl]

It seems Jupyter tries to load a default notebook from this location: "https://usegalaxy.no/static/toolshed/default_notebook.ipynb", but that file did not exist. So I found a notebook somewhere, renamed it to "default_notebook.ipynb" and placed it in the "/srv/galaxy/server/static/toolshed/" directory. Now Jupyter runs without job errors and can be accessed, but there are still problems with some paths inside Jupyter. And I also got warnings about issues with the SSL certificate.

[torfinnnome]

The IT's should all be disabled, for now (I thought I did...). They are spawned using Docker, but cancelling the job in Galaxy does not kill the container running on the Slurm nodes. Which means that we currently end up with an "infinite" number of ITs. Ugly hack: Might be possible to add a time limit using the sorting hat?

I think .EU is using a DockerSwarm for running ITs. Running them all on the head node will probably work, but then we should reallocate some resources (CPU+mem) (and it's not scalable, so I'm not a fan).

[sveinugu]

@torfinnnome We do have a use case right now, but we use the eu server instead, so it is not that urgent. But I think creating the infrastructure for this would be nice once you are back.

[tothuhien]

Seem to be a related issue here: galaxyproject/galaxy#13511