Galaxy Server administration

Here you can learn everything you need to become a Pro Galaxy Administrator! These resources cover everything from setup, to configuration, to monitoring, to customisation.

Galaxy admins chat on Matrix, do not hesitate to ask questions there

  Community Matrix Chat

Administrating your own (small) (local) instance? Other admins are meeting regularly to discuss issues/problems and solutions. If you are interested, check out the webpage:

  Small scale Galaxy Admins Community of Practice Website

Not sure where to start?

Try the Galaxy Server administration Learning Pathway! Start Learning

Material

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

Core

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

Lesson Slides Hands-on Recordings
Ansible
ansible
Galaxy Installation with Ansible
ansible deploying git-gat
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
jobs ansible git-gat
Mapping Jobs to Destinations using TPV
jobs git-gat
Running Jobs on Remote Resources with Pulsar
ansible jobs git-gat
Use Apptainer containers for running Galaxy jobs
jobs ansible git-gat

Data Management & Reference Data

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

Lesson Slides Hands-on Recordings
Alternative Celery Deployment for Galaxy
ansible
Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD)
storage
Data Libraries
ansible storage git-gat
Distributed Object Storage
ansible storage
Reference Data with CVMFS
ansible git-gat
Reference Data with CVMFS without Ansible
Reference Data with Data Managers
Setting up Celery Workers for Galaxy
ansible git-gat

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
ansible automation
Deploying a Beacon v1 in Galaxy
ga4gh beacon git-gat
Enable upload via FTP
data git-gat
External Authentication
authentication
Galaxy Interactive Tools
ansible interactive-tools
Galaxy Tool Management with Ephemeris
tools git-gat
How I learned to stop worrying and love the systemd
ansible systemd
Performant Uploads with TUS
Training Infrastructure as a Service (TIaaS)
ansible training jobs git-gat

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
Galaxy on the Cloud
Galaxy Installation on Kubernetes
kubernetes
Managing Galaxy on Kubernetes
kubernetes
Galaxy usage on SURF Research Cloud
deploying
Pulsar usage on SURF Research Cloud
deploying
Deploying Tailscale/Headscale for private mesh networking
wireguard networking
Deploying Wireguard for private mesh networking
wireguard networking
Deploying a compute cluster in OpenStack via Terraform
terraform deploying cloud

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
git-gat
Customizing the look of Galaxy (Manual)
Galaxy Administrator Time Burden and Technology Usage
deploying maintenance survey
Galaxy Troubleshooting
Gearing towards production
Server Maintenance: Cleanup, Backup, and Restoration
ansible deploying git-gat
Upgrading Galaxy
ansible
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 Telegraf and Grafana
ansible monitoring git-gat
Galaxy Monitoring with gxadmin
monitoring ansible git-gat
Monitoring Galaxy and Pulsar with Sentry
ansible git-gat

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
Galaxy Monitoring with Reports
ansible monitoring git-gat broken
uWSGI

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Create a subdomain for your community on UseGalaxy.eu
subdomain community earth-system interactive-tools
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.

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Community Resources

Community Home Maintainer Home

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoNate Coraor avatar Nate Coraororcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin Čechorcid logoMira Kuntz avatar Mira Kuntz

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

Dawa Ometto avatar Dawa Omettoorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoLucille Delisle avatar Lucille DelisleAbdulrahman Azab avatar Abdulrahman AzabNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoAnthony Bretaudeau avatar Anthony BretaudeauMarius van den Beek avatar Marius van den Beekorcid logoArmin Dadras avatar Armin Dadrasorcid logoSimon Gladman avatar Simon Gladmanorcid logoBérénice Batut avatar Bérénice Batutorcid logoMartin Čech avatar Martin Čechorcid logoPaul De Geest avatar Paul De GeestBartosz Walkowicz avatar Bartosz Walkowiczorcid logoJohn Davis avatar John Davisorcid logoHelena Rasche avatar Helena Rascheorcid logoGianmauro Cuccuru avatar Gianmauro Cuccuruorcid logoPeter van Heusden avatar Peter van HeusdenMélanie Petera avatar Mélanie PeteraCatherine Bromhead avatar Catherine BromheadMatthias Bernt avatar Matthias Berntorcid logoNate Coraor avatar Nate Coraororcid logoLaila Los avatar Laila LosKweyakie Afi Blebo avatar Kweyakie Afi Bleboorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoJohn Chilton avatar John Chiltonorcid logoMira Kuntz avatar Mira KuntzEnis Afgan avatar Enis Afganorcid logoSaskia Hiltemann avatar Saskia HiltemannJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoTomas Klingström avatar Tomas Klingströmorcid logoTorfinn Nome avatar Torfinn NomeNiall Beard avatar Niall BeardMirela Minkova avatar Mirela Minkovaorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzTunc Kayikcioglu avatar Tunc Kayikciogluorcid logoBjörn Grüning avatar Björn GrüningGildas Le Corguillé avatar Gildas Le CorguilléDave B. avatar Dave B.Alex Mahmoud avatar Alex MahmoudPablo Moreno avatar Pablo MorenoMarie Josse avatar Marie Josseorcid logoVlad Visan avatar Vlad Visanorcid logoCristóbal Gallardo avatar Cristóbal GallardoEdwin den Haas avatar Edwin den Haasorcid logoYvan Le Bras avatar Yvan Le BrasValentin Marcon avatar Valentin Marcon

Funding

These individuals or organisations provided funding support for the development of this resource

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SURF
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Melbourne Bioinformatics
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UFR
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ELIXIR Europe
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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Australian BioCommons
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The University of Melbourne
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Fair-Ease
FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.
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de.NBI
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CINECA
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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.