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Third party - Helm templates

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


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

Basic concepts in respect to docker you need to know.


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.


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.


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


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.


There are some prerequisites you need.

  • docker
  • minikube

Useful commands

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


  • 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


  • kubectl get services

    Gets all services from a deployment


  • kubectl get pv

    Gets all persistant volumes

  • kubectl get pvc

    Gets all persistent volume claims


  • kubectl get deployments

    Gets all deployments (comparable with docker-compose)


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

Useful commands

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#

    Then you can upload it by executing:

    • curl -v --user #username#:#password# --upload-file index.yaml name#/index.yml
    • curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz name#/#chart name#-#version#.tgz

    Now you have to add the repository locally to use in your requirements.yaml.

    • helm repo add #repository name#
  • 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