Galaxy Server administration

Resources related to configuration and maintenance of Galaxy servers

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Material

Core

These are the core, foundational topics for the majority of administration in Galaxy.

Lesson Slides Hands-on Recordings
Ansible
Galaxy Installation with Ansible
Galaxy from an administrator's point of view

Jobs & Scheduling

Learn how to use DRMAA and other resources to schedule your jobs on clusters

Lesson Slides Hands-on Recordings
Connecting Galaxy to a compute cluster
Mapping Jobs to Destinations using TPV
Running Jobs on Remote Resources with Pulsar
Use Apptainer containers for running Galaxy jobs

Data Management & Reference Data

Manage data like a pro: tips on scaling to 1PB and more.

Lesson Slides Hands-on Recordings
Data Libraries
Distributed Object Storage
Reference Data with CVMFS
Reference Data with CVMFS without Ansible
Reference Data with Data Managers
Setting up Celery Workers for Galaxy

Further Learning

These topics will let you further expand your knowledge. They all build upon what you learned in the core topics, and many expect that you have a setup identical to the one started in the core trainings.

Lesson Slides Hands-on Recordings
Automation with Jenkins
Deploying a Beacon v1 in Galaxy
Enable upload via FTP
External Authentication
Galaxy Interactive Tools
Galaxy Tool Management with Ephemeris
How I learned to stop worrying and love the systemd
Performant Uploads with TUS
Training Infrastructure as a Service (TIaaS)

Running Galaxy on the Cloud

If acronyms like EKS, EC2, GCP, ECS, K8S mean anything to you, then you've found where your home! Run Galaxy on someone else's computer with Cloud based tutorials

Lesson Slides Hands-on Recordings
Deploying Tailscale/Headscale for private mesh networking
Deploying Wireguard for private mesh networking
Galaxy on the Cloud
Managing Galaxy on Kubernetes
Galaxy Installation on Kubernetes
Deploying a compute cluster in OpenStack via Terraform

Maintaining a Production Galaxy

Deployed Galaxy? Now what? All of the knowledge you need to maintain it long term.

Lesson Slides Hands-on Recordings
Customizing the look of Galaxy
Customizing the look of Galaxy (Manual)
Galaxy Troubleshooting
Gearing towards production
Server Maintenance: Cleanup, Backup, and Restoration
Upgrading Galaxy
User, Role, Group, Quota, and Authentication managment

Monitoring

Monitor Galaxy like UseGalaxy.eu, learn the ins and outs of monitoring

Lesson Slides Hands-on Recordings
Galaxy Monitoring
Galaxy Monitoring with Reports
Galaxy Monitoring with Telegraf and Grafana
Galaxy Monitoring with gxadmin
Monitoring Galaxy and Pulsar with Sentry

Deprecated Tutorials

Please do not run these. They are outdated and for historical, archival purposes only.

Lesson Slides Hands-on Recordings
Advanced customisation of a Galaxy instance
Controlling Galaxy with systemd or Supervisor
uWSGI

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Docker and Galaxy
Empathy
Galactic Database
Galaxy Database schema

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoNate Coraor avatar Nate Coraororcid logoSimon Gladman avatar Simon Gladmanorcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin Čech

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Enis Afgan avatar Enis Afganorcid logoHelena Rasche avatar Helena Rascheorcid logoMartin Čech avatar Martin ČechPablo Moreno avatar Pablo Morenoorcid logoGianmauro Cuccuru avatar Gianmauro Cuccuruorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMira Kuntz avatar Mira Kuntzorcid logoSimon Gladman avatar Simon Gladmanorcid logoNate Coraor avatar Nate CoraorAlex Mahmoud avatar Alex MahmoudMatthias Bernt avatar Matthias BerntMarius van den Beek avatar Marius van den BeekAbdulrahman Azab avatar Abdulrahman AzabCatherine Bromhead avatar Catherine Bromheadorcid logoBérénice Batut avatar Bérénice Batutorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoJohn Davis avatar John DavisNuwan Goonasekera avatar Nuwan GoonasekeraGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLucille Delisle avatar Lucille Delisleorcid logoJohn Chilton avatar John Chiltonorcid logoLaila Los avatar Laila LosEdwin den Haas avatar Edwin den Haasorcid logoTorfinn Nome avatar Torfinn NomeDave B. avatar Dave B.Valentin Marcon avatar Valentin Marconorcid logoNicola Soranzo avatar Nicola Soranzo

Funders

This material was funded by:

Common Infrastructure for National Cohorts in Europe, Canada, and Africa avatar CINECA