Galaxy Helm Chart

Overview

This tutorial describes how to use the Galaxy Helm Chart to deploy a production grade instance of Galaxy on a Kubernetes cluster. The Helm Chart has been designed to follow best practices adopted by the community, including the usegalaxy.* federation, and will install a Galaxy with the following features by default:

• Zero-downtime configuration changes and upgrades
• Scalable web and job handlers
• Automatic failure recovery based on liveness and readiness probes
• A built-in nginx for efficiently serving large files
• TUSD for resumable uploads
• Celery for background jobs
• Access to CVMFS reference data
• A toolset matching the usegalaxy.* federation (also served off CVMFS)
• Interactive tools (wildcard DNS mapping required)
• Minimal privileges, with jobs running as non-root and only having access to datasets they need
• Automatic maintenance scripts to cleanup the galaxy database and tmp directories

Optionally, the chart can be configured with

• High-availability components - this includes trivial scaling of clustered Postgres, Rabbit MQ etc.
• Replacement components - You can replace the built-in operators with a managed or existing Postgres database (e.g. Amazon RDS), RabbitMQ cluster etc.
• Use S3 as an alternative to CVMFS
• Automatic scraping of metrics which can be sent to Influxdb

Agenda

1. Galaxy Helm Chart
   1. Overview
   2. Prerequisites
   3. Deploying the Default Configuration
   4. Setting the admin user and changing the brand
   5. Deleting a Deployed Helm Release
2. Next Steps

Prerequisites

Some familarity with Kubernetes is assumed. This includes general administrative familarity and how to install and configure Helm Charts.

A running Kubernetes cluster is also required (1.27 or higher), with Helm (3.5 or higher) configured to access it. For development and testing purposes this can be easily achieved by installing Docker Desktop locally and enabling Kubernetes. Afterwards, install Helm.

For production deployments, we’ll also need some storage resources for data persistence. This can be done by either defining a storage class or creating a Persistent Volume and a corresponding Persistent Volume Claim. Once created, just keep a note of the resources Persistent Volume Claim ID and to use later.

Deploying the Default Configuration

The default set of values for the Galaxy chart configures only a minimal set of Galaxy options necessary. The configured options are required for suitable operation of the system. Setting other options will depend on the environment and it’s best to refer to the general Galaxy documentation; we’ll also take a look at how to make configuration changes in the context of the chart later in this tutorial.

Hands-on: Deploying the Galaxy Helm Chart

1. First, we need to add the helm repository for the chart. The chart is automatically packaged, versioned and uploaded to a helm repository on github with each accepted PR. Therefore, the latest version of the chart can be directly installed from that repository.

   helm repo add galaxyproject https://raw.githubusercontent.com/galaxyproject/helm-charts/master/
   helm repo update
   

2. We can now deploy Galaxy via the Chart. Running this command will create a new Helm release (i.e., chart installation) called mygalaxy.

   helm install mygalaxy galaxyproject/galaxy
   

3. It will take about a minute or two for the necessary containers to download, the database to initialize, and Galaxy processes to start. Ultimately, while this may depend on the Kubernetes cluster setup you are using, Galaxy should be available at https:///galaxy for the given machine. We can always check the status of our release by typing `helm status galaxy`.

Setting the admin user and changing the brand

The chart is designed to follow standard Kubernetes and Helm idioms, and therefore, it should be intuitively similar to the steps required to change configuration in any other Helm chart. For example, ingress paths, resource allocations, container images etc. can be changed following standard helm conventions. The list of available configuration options are also documented in the Galaxy Helm Chart repository

To change Galaxy specific configuration, such as setting the admin user or change the brand in galaxy.yml, we can follow the following steps. Once done, we will also rollback our change to demonstrate how Helm manages configuration.

Hands-on: Setting admin user and changing the brand

1. Modify the following entries in your mygalaxy.yml. Make sure to add these keys under the configs: section of the file.

   configs:
     galaxy.yml:
       galaxy:
         brand: "Hello World"
         admin_users: "admin@mydomain.com"
   

2. Now, let’s upgrade the chart to apply the new configuration.

   helm upgrade --reuse-values -f mygalaxy.yml mygalaxy galaxyproject/galaxy
   

3. Inspect the currently set Helm values by:

   helm get values mygalaxy
   

4. List the installed Helm charts again and note that the revision of the chart has changed as expected.

   helm list
   NAME  	  REVISION	UPDATED                 	STATUS  	CHART                 	APP VERSION	NAMESPACE
   mygalaxy	2       	Wed Jun 26 14:51:17 2023	DEPLOYED	galaxy-5.14.2          	v24.0.2    	default
   

5. Revisit the Galaxy Application in your browser to check whether the settings have changed. This will take a short while (< 1 minute) for the new container to come up. You should experience no downtime.

6. Let’s now roll back to the previous revision.

   helm rollback mygalaxy 1
   

   Use helm get values again to observe that the values have reverted to the previous revision. After a short while, once the new container is up and running, Kubernetes will automatically switch over to it and you can see that the previous configuration has been restored.

Deleting a Deployed Helm Release

By default, the Helm chart is designed to install all required dependencies, so that it’s easy to get an instance up and running quickly for experimentation. However, in production, we recommend installing the dependency charts separately, once per cluster, by installing Galaxy with helm options --set postgresql.deploy=false --set s3csi.deploy=false --set cvmfs.deploy=false --set rabbitmq.deploy=false.

This is particularly important during uninstallation, where orderly destruction of dependencies is often required For example, if the rabbitmq operator is uninstalled before the rest of the Galaxy helm chart is deleted, there will be no operator left to cleanup rabbitmq resources. Installing the aforementioned operators separately sidesteps this problem.

Hands-on: Deleting a Deployed Helm Release

   helm delete mygalaxy
   helm delete mycvmfs # and any other operators

Next Steps

This tutorial covers the basics of getting Galaxy deployed on Kubernetes using Helm. There is a lot more to understanding all the configuration options for the chart and the available deployment models. For more info on some of these topics, take a look at the Galaxy Helm chart repository as well as other tutorials tagged with kubernetes. Also, feel free to reach out on Gitter: https://gitter.im/galaxyproject/FederatedGalaxy.

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Key points

• Stock deployment of production Galaxy components on Kubernetes is simple

• Helm chart allows easy configuration changes

Frequently Asked Questions

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Citing this Tutorial

1. Pablo Moreno, Enis Afgan, Nuwan Goonasekera, Alex Mahmoud, John Davis, Galaxy Installation on Kubernetes (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/k8s-deploying-galaxy/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{admin-k8s-deploying-galaxy,
author = "Pablo Moreno and Enis Afgan and Nuwan Goonasekera and Alex Mahmoud and John Davis",
	title = "Galaxy Installation on Kubernetes (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/k8s-deploying-galaxy/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Go Further

Do you want to extend your knowledge? Follow one of our recommended follow-up trainings:

• tutorial Hands-on: Managing Galaxy on Kubernetes

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-deploying-galaxy/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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