Update pipelines3 system setup script

[n1zea144]

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

The following script is updated:
https://github.mskcc.org/knowledgesystems/portal-configuration/blob/master/eks-cluster/pipelines/setup_system_dependencies.sh

Technical Description (How are we going to achieve the above)

Per Rob:

We do install software and tools and such via the system setup/install script we have here: https://github.mskcc.org/knowledgesystems/portal-configuration/blob/master/eks-cluster/pipelines/setup_system_dependencies.sh .. although I think this is out of date and needs to be updated. For one thing, it does not install a python3 interpreter as far as I can tell ... and our current pipelines3 node is running python 3.7, which has passed end of life. It also does not install openjdk21, which we need. There are other configuration issues ... such as the accounts which allow triggering a run of the public importer, or the triage importer. Ideally all of these things should be checked in to the setup script and we should be able to run on an ephemerally launched node.

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes