inst/README.md

In Bioconductor/BiocKubeInstall: Build R / Bioconductor package binaries using Kubernetes on a cloud service

BiocKubeInstall - Kubernetes application to create Bioconductor package binaries

Author:

1. Martin Morgan

2. Nitesh Turaga

This kubernetes app is used to create binary packages for Bioconductor and store them on Google cloud storage.

Docker images

The image for the manager is pod is built from the file Dockerfile.manager and is available on the Bioconductor organization page on Dockerhub as,

bioconductor/bioc-redis:manager

The images for the worker pods are build from the files under the following pattern, Dockerfile.worker.RELEASE_X_Y. For example, the image for the worker for Bioconductor release 3.12 is under Dockerfile.worker.RELEASE_3_12. These images are available on Dockerhub as

bioconductor/bioc-redis:RELEASE_3_13

bioconductor/bioc-redis:RELEASE_3_12

To build the docker images locally,

docker build -t bioconductor/bioc-redis:manager -f \
    docker/Dockerfile.manager docker

docker build -t bioconductor/bioc-redis-worker:RELEASE_3_12 -f \
    docker/Dockerfile.worker.RELEASE_3_12 docker

The docker images are build on top of the bioconductor/bioconductor_docker images. The manager node inherits from the devel image, and the worker nodes inherit from the respective Bioconductor release version needed for packages, i.e, RELEASE_3_12 or RELEASE_3_13 and so on.

The manager image has Google cloud SDK installed along with some settings for Redis which are not needed on the worker image.

NFS server

The manager pod and the worker pods share an NFS server as a volume mount in this K8s application. The volume mount logic and code is taken from the kubernetes examples given at this link:

https://github.com/kubernetes/examples/tree/master/staging/volumes/nfs

Quick start for k8sredis build binaries

Assumption: The user has a service account key from project with permission as Storage account admin. Refer to vignette from https://github.com/Bioconductor/BiocKubeInstall package for more details

Step 0: Start k8s cluster on GCE

gcloud container clusters create \
    --zone us-east1-b \
    --num-nodes 4 \
    --enable-autoscaling \
    --min-nodes 1 \
    --max-nodes 6 \
    --machine-type=e2-standard-4 niteshk8scluster

gcloud container clusters get-credentials niteshk8scluster

Step 1: Start service NFS using this commands

kubectl apply -f k8s/nfs-volume/

Step 2: Create a kubectl secret. You must have the file bioc-binaries.json on your local machine. To create a kubernetes secret and download it you need to be a service account admin. Please refer to the documentation refering to Create kubernetes secret.

kubectl create secret generic \
    bioc-binaries-service-account-auth \
    --from-file=service_account_key=bioc-binaries.json

## Describe key
kubectl describe secrets/bioc-binaries-service-account-auth

Step 3: Start Redis, Rstudio, Manager and worker pods

kubectl apply -f k8s/bioc-redis/

Step 4: Delete cluster

kubectl delete -f k8s/bioc-redis/
kubectl delete -f k8s/nfs-volume/

gcloud container clusters delete niteshk8scluster

Logging into a pod

kubectl exec --stdin --tty pod/manager -- /bin/bash

Create kubernetes secret

Create a service account key. The service account key has 'Storage Admin' permissions, so it can upload the binaries to a google bucket.

## Create service account
gcloud iam service-accounts create bioc-binaries \
   --display-name "Storage Admin SA" \
   --description "Bioc Binaries storage admin"

## List service account
gcloud iam service-accounts list \
    --filter [e-mail]

## Download service account key locally
gcloud iam service-accounts keys create \
    bioc-binaries.json \
    --iam-account [e-mail]

## Add 'Storage Admin' role to service account.
gcloud projects add-iam-policy-binding fancy-house-303821 \
    --member \
    "serviceAccount:[e-mail]" \
    --role "roles/storage.admin"

Detailed launch sequence of the K8s app (not recommended)

Launch the NFS server first,

kubectl create -f k8s/nfs-server-gce-pv.yaml
kubectl create -f k8s/nfs-server-rc.yaml
kubectl create -f k8s/nfs-server-service.yaml
kubectl create -f k8s/nfs-pv.yaml
kubectl create -f k8s/nfs-pvc.yaml

then the bioc-redis application,

kubectl create -f k8s/bioc-redis/rstudio-service.yaml
kubectl create -f k8s/bioc-redis/redis-service.yaml
kubectl create -f k8s/bioc-redis/redis-pod.yaml
kubectl create -f k8s/bioc-redis/manager-pod.yaml
kubectl create -f k8s/bioc-redis/worker-jobs.yaml

Bioconductor/BiocKubeInstall documentation built on Jan. 26, 2023, 12:35 a.m.