fdlk / datashield-helm

A Helm repository to setup Opal and RStudio as central analysis server

DataSHIELD - Helm templates

These are the Helm templates that we will use for DataSHIELD operations.

Content

This deployment repository consists of 3 charts.

• Opal

  Opal depends on: mongodb, mysql and rserver. You can choose to deploy MySQL or MongoDB and you have to deploy RServer. The last one is mandatory dependency.

• RServer

  This is the R environment used for all the DataSHIElD actions.

• RStudio

  This will be the analysis server.

Deployment

When you want to use kubernetes there are some commands you need to know. Also running on a remote cluster will be a must have to control your whole DTAP.

Basic concepts kubernetes

Basic concepts in respect to docker you need to know.

Deployments

Are a set of pods that will be deployed according to configuration that is usually managed bij Helm. These pods interact with eachother by being in the same namespace created by kubernetes according to the deployment configuration.

Pods

A pod is wrapper around a container. It will recreate the container when it is shutdown for some reason and interact with other pods when needed.

Containers

A container is a docker-container that is created from a docker image. It could be seen as an VM for example

Images

An image is a template for a container some sort of boot script but also contains the os for example. A build dockerfile, if you will.

Prerequisites

There are some prerequisites you need.

• docker
• minikube

Useful commands

Commands that can be used to get information from a kubernetes cluster

Pods

• kubectl get pods (optional: [--all-namspaces])

  Gets alls running instances of containers from a certain deployment

• kubectl describe pod #pod name# --namespace=#namesspace#

  Describes the pod initialization, also displays error messages more accurately if they occur

• kubectl remove pod #pod name# --namespace=#namespace# (optional: [--force] [--grace-period=0])

  Removes a pod from the system (but will restart if the option is set in the deployment,yaml [see note]).

  note: You can not do this while the deployment of the service is still there

Services

• kubectl get services

  Gets all services from a deployment

Volumes

• kubectl get pv

  Gets all persistant volumes

• kubectl get pvc

  Gets all persistent volume claims

Deployments

• kubectl get deployments

  Gets all deployments (comparable with docker-compose)

Helm

This repository is serves also as a catalogue for Rancher. We have several apps that are served through this repository. e.g.

• Opal
• Opal

Development

You can you need to know to easily develop and deploy helm-charts

• helm lint .

  To test your helm chart for code errors.

• helm install . --dry-run --debug

  Check if your configuration deploys on a kubernetes cluster and check the configuration

• helm install . #release name# --namespace #remote namespace#

  Do it in the root of the project where the Chart.yaml is located It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository

• helm package .

  You can create a package which can be uploaded in the molgenis helm repository

• helm publish You still have to create an index.yaml for the chart. You can do this by executing this command: helm repo index #directory name of helm chart#

• helm dep build

  You can build your dependencies (create a charts directory and install the chart in it) of the helm-chart.

• helm list

  Lists all installed releases

• helm delete #release#

  Performs a sort of mvn clean on your workspace. Very handy for zombie persistent volumes or claims.

• install tiller on remote cluster

  To install tiller on a remote cluster you need an rbac-config.yml. kubectl create -f rbac-config.yaml

  When you have defined the yaml you can add the tiller to the cluster by following the steps below. helm init --service-account tiller