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MOLGENIS Helm templates
These are the Helm templates that we will use for MOLGENIS operations. 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.
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.
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)
When you want to see what is running on the clusters at the CIT you have to make a context switch.
You can access the cluster with kubeconfig-files. You can obtain these by downloading them from the
MOLGENIS kubernetes cluster.
Go to https://rancher.molgenis.org:7777 and login
Go to Rancher --> Cluster: #name# --> Kubeconfig File
Go to a Terminal where
Add this configuration to ~/.kube/config (or place a new file besides this one)
# When you added the MOLGENIS configuration to the original configuration kubectl config use-context molgenis # or when you placed the MOLGENIS configuration besides the original one kubectl config use-context molgenis --kubeconfig=*full path to molgenis config*
You can now access all facilities of the MOLGENIS cluster like it is running locally
kubectl get pods --namespace=*#namespace of application#*
This repository is serves also as a catalogue for Rancher. We have serveral apps that are served through this repoistory. e.g.
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
You still have to create an
index.yamlfor 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 https://registry.molgenis.org/repository/helm/#chart name#/index.yml
curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz
Now you have to add the repository locally to use in your
helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis
helm dep build
You can build your dependencies (create a
chartsdirectory and install the chart in it) of the helm-chart.
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