Shiny deployment for on Kubernetes (Nautilus)
This assumes the you already have a fully dockerized version of the shiny app. A complete example is provided in the app dir here, adjust as needed. Have the Docker image pre-built and published to GitHub Container registry (as in this demo repo -- merely copy the .github folder). Alternately, you can have the image build via the Nautilus GitLab and deployed to its container registry.
Deploying on Kubernetes involves three components: a deployment specifying the environment (Docker image, environmental variables, computational resources), an ingress specifying the external URL (and handling https secure config), and a service connecting the two. See the Nautilus docs.
- Edit
deployment.yamlto point to your desired Dockerimage. Optionally rename the k8s-app (shiny-app), and optionally set resource and environmental variables. - Edit the
ingress.yamlto specify the host URL (e.g. if your namespace iseco4cast, I recommendshiny-eco4cast.nrp-nautilus.io. Thenrp-natuilus.iopart is needed, and the prefix to it should not have.. I recommen using the namespace in the prefix to avoid collisions; theshiny-part is just a suggestion.) - Edit the
service.yamlto match the names of pod. Note the spec.ports.targetPort section should match the port exposed in the Dockerfile for the app.
Bring up all components (from up.sh), modifying to your namespace:
kubectl apply -f service.yaml -n biodiversity
kubectl apply -f ingress.yaml -n biodiversity
kubectl apply -f deployment.yaml -n biodiversityIt may take a few minutes for the deployment to spin up a pod serving the app. Check the status with kubectl get pods, kubectl describe pod shiny-deployment-xxxx (replace xxxx with the suffix shown by get pods) etc. The deployment will stay up for up 2 weeks before being auto-culled. You can refresh the deployment as needed. Delete the existing depoyment with down.sh recipe (you will first need to adjust the namespace and containers appropriately.)