Admin Training Course

Comment: What is a Learning Pathway?
A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.

Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway will guide you through all the steps required to setup your own Galaxy server with Ansible, configuring it, and making it production ready.

This learning path covers all the topics usually taught during the regular 5-day admin training workshops. Each module represents what is usually roughly taught in one day during the events.

Monday: Setting up Galaxy with Ansible

This module covers getting a Galaxy server setup with Ansible, a server you will develop furhter in the rest of the modules

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

Tuesday: Making the server useful

Here we pivot to focus on making our server useful; adding tools and data, configuring quotas and authentication

Lesson Slides Hands-on Recordings
Server Maintenance: Cleanup, Backup, and Restoration
Reference Data with CVMFS
Reference Data with Data Managers
Use Apptainer containers for running Galaxy jobs
Galaxy Tool Management with Ephemeris
User, Role, Group, Quota, and Authentication managment
Data Libraries
Scripting Galaxy using the API and BioBlend

Wednesday: Clusters

Lesson Slides Hands-on Recordings
Connecting Galaxy to a compute cluster
job_conf.xml external-link
Mapping Jobs to Destinations using TPV
Running Jobs on Remote Resources with Pulsar

Thursday: Expanding

Lesson Slides Hands-on Recordings
Setting up Celery Workers for Galaxy
Training Infrastructure as a Service (TIaaS)
Galaxy Monitoring with Reports
Galaxy Monitoring with gxadmin
Galaxy Monitoring with Telegraf and Grafana
Monitoring Galaxy and Pulsar with Sentry

Friday: Grab bag

Here we have some additional topics, some of which are not admin related. Please feel free to pick and choose the tutorials that are interesting for you.

Lesson Slides Hands-on Recordings
Galaxy Troubleshooting
Tool development and integration into Galaxy
Multisample Analysis
Rule Based Uploader
Creating a new tutorial
Galaxy Interactive Tools

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 Gladman