Computational Genomics Kubernetes Installation

The Computation Genomics Group has a Kubernetes Cluster running on several large instances in AWS.

Getting Authorized to Connect

If you require access to this kubernetes cluster, contact Benedict Paten asking for permission to use it, then pass on that permission via email to:

cluster-admin@soe.ucsc.edu

Let us know which group you are with and we can authorize you to use the cluster in the correct namespace.

Authenticating to Kubernetes

We will authorize (authz) you to use the cluster on the server side, but you will also need to authenticate (authn) using your '@ucsc.edu' email address and a unique Java Web token. These credentials are installed in ~/.kube/config in whatever machine you are coming from to get to the cluster.

To authenticate and get your base kubernetes configuration, go to this URL (below), which will ask you to authenticate to Google. Use your '@ucsc.edu' email address as the login. It will then ask you to authenticate via CruzID Gold if your web browser doesn't already have the authentication token cached:

https://cg-kube-auth.gi.ucsc.edu

Once you authenticate, it will pass you back to the 'https://cg-kube-auth.gi.ucsc.edu' website and it should confirm authentication on the top with a message saying "Successfully Authenticated". If you see any errors in red, but are sure you typed in your password and 2-factor auth correctly, click on the above link again and authenticate a second time, which should work. There is a quirk where the web token doesn't always pass back to us correctly on the first try.

Upon success, you will be able to click the blue "Download Config File" button, which contains your initial kubernetes config file. Copy this file to your home directory as ~/.kube/config. Follow the directions on the web page to insert your "namespace:" line as directed. We will let you know which namespace to use.

Testing Connectivity

Once your ~/.kube/config file is set up correctly, you should be able to connect to the cluster. All our shared servers here at the Genomics Institute have the 'kubectl' command installed on them, but if you are coming from somewhere else, just make sure the "kubectl" utility is installed on that machine.

A quick test should go as follows:

$ kubectl get nodes
NAME          STATUS   ROLES    AGE   VERSION
k1.kube       Ready    <none>   13h   v1.15.3
k2.kube       Ready    <none>   13h   v1.15.3
master.kube   Ready    master   13h   v1.15.3