# Deploy on Kubernetes

# Prerequisites

Official cBioPortal Helm chart can be used to easily deploy an instance on a Kubernetes cluster. Make sure you meet the following prerequisites before continuing with the usage instructions:

You have access to a cluster (e.g. Minikube or AWS EKS). We recommend setting up a Minikube cluster on your local machine for development purposes.
You have installed Helm on your system.
You have read and write access to a mysql database server.

# Usage instructions

# Cluster & Database Setup

# Step 1 - Add cBioPortal label to your cluster

Make sure your cluster is already set up and you have access to a node running on it. Instructions for this can vary, depending on your Kubernetes provider. Once your cluster is active, run the following command to add a label to the node on your cluster.

kubectl label nodes <your-node-name> node-group=cbioportal

# Step 2 - Export database access credentials

cBioPortal needs access to a mysql database server hosting cancer study data. As mentioned in the prerequisites, you need access to a mysql database server for this. Instructions for this can vary, depending on your database server provider. Once you have a server available, download MSK's latest database dump here and add the data to your database server. Then, continue with the instructions below using your mysql server credentials.

Create a new values file called values.secret.yaml and add your database credential values.

container:
    env:
        - name: DB_USER
          value: <your-db-user>
        - name: DB_PASSWORD
          value: <your-db-password>
        - name: DB_CONNECTION_STRING
          value: <your-db-connection_string>

# Install cBioPortal

Now that your cluster and data sources have been successfully configured, you can install the cBioPortal helm chart.

# Step 1 - Install Helm Chart

Add repository.

helm repo add cbioportal https://cbioportal.github.io/cbioportal-helm/

Install chart

helm install my-cbioportal cbioportal/cbioportal --version 0.1.6 -f path/to/values.secret.yaml

You should see something similar to this, indicating that the installation was successful.

NAME: my-cbioportal
LAST DEPLOYED: Thu Nov 14 14:15:18 2024
NAMESPACE: default
STATUS: deployed
REVISION: 1
TEST SUITE: None

# Step 2 - Access cBioPortal through localhost

Run the following command to port-forward cBioPortal from the cluster to your local network.

kubectl port-forward deployment/cbioportal 10000:8080

cBioPortal should now be available at localhost on port 10000. Navigate to http://localhost:10000 in your browser to view it.