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Kubernetes deployment of proTES

The files under this directory can be used to deploy proTES on Kubernetes. The deployment method is based on Helm (v3). The directory structure is as follows:

  • templates: YAML files used in Kubernetes clusters where this is deployed
    • mongodb: YAML files for deploying MongoDB.
    • rabbitmq: YAML files for deploying RabbitMQ.
    • protes: YAML files for deploying the proTES server and Celery worker.
    • flower: YAML files for deploying flower (for montoring rabbitmq).
  • values.yaml: contains the configuration variables for the Helm chart.
  • Chart.yaml: the Helm chart metadata.

Usage

First you must create a namespace in Kubernetes in which to deploy proTES. The commands below assume that everything is created in the context of this namespace. How the namespace is created depends on the cluster, so we won't document it here.

Make sure you have both the Kubernetes client (kubectl) and Helm v3 installed. (See https://helm.sh/docs/intro/install/)

Clone this repository:

git clone https://github.com/elixir-europe/proTES/

Tweaks

Update the configuration by modifying the values.yaml file:

cd proTES/deployment
vim values.yaml

NOTE: update the variable clusterType in values.yaml depending on your target cluster:

  • For OpenShift clusters set the value to: openshift
  • For plain Kubernetes clusters set the value to: kubernetes

Using the Helm CLI

Optionally, for CI/CD use cases for example, you could override the values in values.yaml when creating the Helm chart. For example:

cd deployment
helm install . --generate-name --set protes.appName=proxyT

where proxyT will be the name of the proTES deployment and associated objects.

Deployment

After this you can deploy proTES using Helm:

cd deployment
helm install . --generate-name

Once proTES is deployed, you can access it via the url endpoint which you can query by running:

# In vanilla kubernetes clusters
kubectl get ingress

# In OpenShift clusters
kubectl get routes