inst/deploy/common_commands.md

In dynverse/dynguidelines: User guidelines for trajectory inference

Kubernetes

Set context

Make sure this is correct, otherwise everything will time out

kubectl config use-context gke_dynguidelines_us-central1-a_dynguidelines

Rollout

Go to correct folder

cd inst/deploy

Change current version tag (necessary to do rolling updates on google cloud)

export version=`R --vanilla -e  "cat(as.character(packageVersion('dynguidelines'))[[1]]);cat('\n')" | grep "^[^>]" | tail -n 1`
echo $version

Build the container

# without cache:
# docker build --no-cache --build-arg CACHE_DATE=$(date +%Y-%m-%d:%H:%M:%S) -t dynverse/dynguidelines_server:${version} .

# with cache
docker build -t dynverse/dynguidelines_server:${version} inst/deploy

Push the container

docker push dynverse/dynguidelines_server:${version}

Run the container locally for testing

docker run --rm -p 8080:8080 --name shiny dynverse/dynguidelines_server:${version}
docker kill shiny

Push to google cloud

docker tag dynverse/dynguidelines_server:${version} gcr.io/dynguidelines/dynguidelines_server:${version}
docker push -- gcr.io/dynguidelines/dynguidelines_server:${version}
kubectl set image deployment/dynguidelines dynguidelines=gcr.io/dynguidelines/dynguidelines_server:${version}

Get rollout status

kubectl rollout status deployment/dynguidelines
kubectl get deployments

Create cluster from scratch

Add the cluster as a google cloud context: https://cloud.google.com/kubernetes-engine/docs/tutorials/hello-app

Create the cluster

gcloud container clusters create dynguidelines --num-nodes=1

Push container (see up)

Run container

kubectl run dynguidelines --image=gcr.io/dynguidelines/dynguidelines_server:${version} --port 8080

kubectl expose deployment dynguidelines --type=LoadBalancer --port 80 --target-port 8080

Get public ip

kubectl get service

Continuous deployment

Create a service account: https://cloud.google.com/iam/docs/creating-managing-service-accounts#creating_a_service_account

Generate key

Base 64 key

base64 ~/Downloads/dynguidelines-465c5aa876d4.json > /tmp/decrypted_key.json

Add as GCLOUD_SERVICE_KEY to travis environment variables

dynverse/dynguidelines documentation built on July 4, 2020, 9:09 p.m.