Deploy a Shiny app to Google Kubernetes Engine

2022-03-26

If you have a Shiny app and a Google Kubernetes Engine (GKE) instance you can automate deployment of that app upon each git commit.

Each commit the buildsteps need to re-build the Docker container with the Shiny app code and environment, then deploy it to the GKE instance.

Dockerfile

Assuming you have a shiny app in ./shiny/ relative to the Dockerfile, then a Dockerfile could look like:

FROM rocker/shiny

# install R package dependencies
RUN apt-get update && apt-get install -y \
    libssl-dev \
    ## clean up
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/ \
    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

## Install packages from CRAN
RUN install2.r --error \
    -r 'http://cran.rstudio.com' \
        remotes \
        shinyjs \
    ## install Github packages
    && installGithub.r MarkEdmondson1234/googleCloudRunner \
    ## clean up
    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

## assume shiny app is in build folder /shiny
COPY ./shiny/ /srv/shiny-server/my-app/

Depending on how your ingress is setup, this would appear on your Kubernetes cluster at /my-app/ - see this blog post on details for setting up R on Kubernetes

Kubernetes deployment file

You can then also have a deployment file for Kubernetes that will govern its configuration after the new docker image is built. An example deployment file is below:

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: shiny-your-app
spec:
  replicas: 1
  selector:
    matchLabels:
      run: shiny-your-app
  strategy:
    rollingUpdate:
      maxSurge: 1
      maxUnavailable: 1
    type: RollingUpdate
  template:
    metadata:
      labels:
        run: shiny-your-app
    spec:
      nodeSelector:
        cloud.google.com/gke-nodepool: generic-compute-pool
      volumes:
      - name: varlog
        emptyDir:
      containers:
      - name: shiny-your-app
        image: gcr.io/your-project/shiny-your-app:latest
        ports:
        - containerPort: 3838
        volumeMounts:
        - name: varlog
          mountPath: /var/log/shiny-server/

Cloud Build

Your cloudbuild steps will then build the Dockerfile, then use gcr.io/cloud-builders/gke-deploy to deploy it to the cluster - see this Google guide on deployment to GKE via Cloud Build for details

library(googleCloudRunner)

bs <- c(
  cr_buildstep_docker("shiny-your-app",
                      tag = c("latest","$SHORT_SHA"),
                      kaniko_cache = TRUE),
  cr_buildstep("gke-deploy",
               args = c("run",
                        "--filename=deployment-k8s.yml",
                        "--image=gcr.io/$PROJECT_ID/shiny-your-app:$SHORT_SHA",
                        "--location=europe-west1-b",
                        "--cluster=your-k8s-cluster"))
)

yaml <- cr_build_yaml(steps = bs)
cr_build_write(yaml, "build/cloudbuild.yml")

In this example we write the cloudbuild.yml to a build folder rather than making an inline build trigger deployment. This is setup in a Build Trigger upon GitHub commit with the code below:

repo <- cr_buildtrigger_repo("your-name/your-repo-with-shiny")

# test build by pushing to git after this trigger made
cr_buildtrigger("build/cloudbuild.yml",
                name = "deploy-my-shiny-app",
                trigger = repo)

All together the git repo folder looks like:

|
|- build/
   | - cloudbuild.yml
|- deployment-k8s.yml
|- Dockerfile
|- shiny/
   | - app.R

As you update the code in app.R and push to GitHub, the build trigger builds the Docker image and publishes it to the kubernetes cluster. The docker is built using kaniko cache, which speeds up repeat builds and deployments.