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 () and tutorial () buttons below.

Material

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
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
Deploying Tailscale/Headscale for private mesh networking
wireguard networking
Deploying Wireguard for private mesh networking
wireguard networking
Galaxy on the Cloud
Managing Galaxy on Kubernetes
kubernetes
Galaxy Installation on Kubernetes
kubernetes
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 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 Reports
ansible monitoring git-gat broken
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
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 logoAvatarHelena Rascheorcid logoAvatarNate Coraororcid logoAvatarSimon Gladmanorcid logoAvatarBjörn Grüningorcid logoAvatarMartin 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:

AvatarPablo MorenoAvatarCatherine BromheadAvatarEnis AfganAvatarAlex MahmoudAvatarGildas Le Corguilléorcid logoAvatarJohn Chiltonorcid logoAvatarAnthony BretaudeauAvatarMatthias Berntorcid logoAvatarHelena RascheAvatarDave B.orcid logoAvatarLucille Delisleorcid logoAvatarMartin Čechorcid logoAvatarNate Coraororcid logoAvatarDaniel Blankenbergorcid logoAvatarJohn Davisorcid logoAvatarSaskia HiltemannAvatarNuwan Goonasekeraorcid logoAvatarBérénice Batutorcid logoAvatarBjörn Grüningorcid logoAvatarSimon Gladmanorcid logoAvatarNicola Soranzoorcid logoAvatarHans-Rudolf Hotzorcid logoAvatarTorfinn NomeAvatarMarius van den BeekAvatarValentin Marconorcid logoAvatarGianmauro CuccuruAvatarAbdulrahman Azaborcid logoAvatarMira Kuntzorcid logoAvatarLaila Los

Funders

This material was funded by:

AvatarCommon Infrastructure for National Cohorts in Europe, Canada, and Africa