OncoKB

All ConfigMaps and Secrets for oncokb-eu cluster are under oncokb-deployment repo. For all other cluster, config/secrets can be found in portal-configuration repo

System Architecture

Editable board is located here https://miro.com/app/board/uXjVMTJ_gKI=/

Clusters

• cbioportal-prod/oncokb This is the shared account with cBioPortal which serves the OncoKB public apps that running behind oncokb.org. The cluster is under us-east-1.

• oncokb-eu/default This is a cluster served under eu-central-1 region.

• oncokb-dev/default This is the MSK dev cluster. Account: msk-oncokb-dev (762447640649)

• oncokb-production/default This is the MSK production cluster. Account: msk-oncokb-prod (084637913395)

Manage clusters

• All clusters are served under AWS/EKS. We use ArgoCD to sync and deploy applications.
• All clusters use the default namespace to serve apps except the cbioportal-prod which is oncokb.
• OncoKB cluster versions are managed by Terraform.
• We use helm(v3.5.2) to install charts.

Services

Redis

• We currently only use Redis Cluster in production.
• Managed by ArgoCD. Find appropriate cluster here

Airflow

• We have two versions of airflow running.
  • airflow.oncokb.org
  • airflow.oncokb.aws.mskcc.org
• The dags are located at https://github.com/oncokb/oncokb-pipeline/tree/master/oncokb-airflow/oncokb

Prometheus/Grafana

• Managed by ArgoCD, see HERE

Notes

Creating a new subdomain

To add a subdomain of oncokb.org, please follow the steps below:

1. Add host under spec.hosts in ingress/ingress_oncokb.yml

2. Under the same yaml file, add rule to handle traffic to the subdomain

3. Add k8s Service and Deployment under oncokb folder. The service name should be the same as the step 2. You can use oncokb/oncokb_public.yaml file as an example

4. Commit changes to GitHub

5. Login to ArgoCD Web and sync