2025 Galaxy Admin Training (Brno)
In-person course
The ins and outs of setting up your own production quality Galaxy server
This workshop will cover basic and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community.
Galaxy is an open web based platform for data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of research domains.
Schedule
Please see the Program tab
Prerequisites
Please see the Setup tab
Registration
Please apply via our registration form. We only have limited space so please register as soon as possible.
Please feel free to contact us at galaxy@cesnet.cz if you have any question and check this site for any updates.
Logistics
Venue
The Admin training will be held in CESNET offices, Brno, Czechia (map). The venue is in the city centre of Brno, which is an amazing city to visit, see https://www.gotobrno.cz/.
Accommodation
There are many affordable hotels around and also plenty of opportunity for private accommodation. There is no organised effort or group reservation. If you are unsure where to book some tips for generic hotels nearby are: Continental, Avanti, and Cosmopolitan.
Getting to Brno
- By train - Plenty of trains arriving in Brno from all of Europe. The venue is 10 mins tram ride from the main train station.
- By plane - Generally fly to Prague or Vienna and take a train or bus to Brno. There is a couple of flights landing in Brno directly but they are rare.
- By car - Plenty of highways, drive safely.
Getting Around
There is serious amount of public transportation available that will get you anywhere. Use Google Maps or https://mapy.com/en to find connections and use your card, phone, watch and any other contactless payment device to easily pay for it when entering the vehicle (details at https://www.pipniajed.cz/en.html).
Who is this course for?
Galaxy administrators, or anyone interested in running a Galaxy serverEvent Location
Geocoding via Nominatim, Map data from OpenStreetMap
Organisers & Instructors
This event is brought to you by:
| Organiser(s) |
 
Martin Čech
|
| Instructor(s) |
Marius van den Beek
Björn Grüning
Mira Kuntz
Martin Čech
Martin Demko
|
| Infrastructure |
Before you start
Before starting the course, make sure to follow the setup instructions
Monday: Setting up Galaxy with Ansible
This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:00 - 09:30 |
Registration |
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09:30 - 10:00 |
Welcome and Introduction |
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Galaxy from an administrator's point of view
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| Ansible | ||||
11:30 - 11:45 |
Break |
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13:00 |
Galaxy Installation with Ansible | |||
13:00 - 14:00 |
Lunch |
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15:00 - 15:30 |
Break |
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| Server Maintenance: Cleanup, Backup, and Restoration | ||||
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Advanced customisation of a Galaxy instance
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17:00 |
Wrap Up and Close |
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Tuesday: Making the server useful
Today we pivot to focus on making that server useful: adding tools and data, configuring quotas, etc.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:30 - 10:00 |
Welcome and Recap |
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Performant Uploads with TUS
|
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Reference Data with Data Managers
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| Reference Data with CVMFS | ||||
11:30 - 11:45 |
Break |
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| Use Apptainer containers for running Galaxy jobs | ||||
| Galaxy Tool Management with Ephemeris | ||||
13:00 - 14:00 |
Lunch |
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| Data Libraries | ||||
15:00 - 15:30 |
Break |
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15:00 - 15:30 |
Break |
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Scripting Galaxy using the API and BioBlend
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17:00 |
Wrap Up and Close |
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Wednesday: Clusters
Today we focus on connecting the Galaxy server to a compute cluster, and explore job configuration and TPV
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:30 - 10:00 |
Welcome and Recap |
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User, Role, Group, Quota, and Authentication managment
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| Connecting Galaxy to a compute cluster | ||||
11:30 - 11:45 |
Break |
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| Mapping Jobs to Destinations using TPV | ||||
13:00 - 14:00 |
Lunch |
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| Running Jobs on Remote Resources with Pulsar | ||||
15:00 - 15:30 |
Break |
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17:00 |
Wrap Up and Close |
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Thursday: Expanding
Today we focus on running jobs on remote resources, then look into monitoring, data uploads, etc.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:30 - 10:00 |
Welcome and Recap |
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| Setting up Celery Workers for Galaxy | ||||
| Galaxy Monitoring with Reports | ||||
| Galaxy Monitoring with Telegraf and Grafana | ||||
11:30 - 11:45 |
Break |
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| Galaxy Monitoring with gxadmin | ||||
13:00 - 14:00 |
Lunch |
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| Training Infrastructure as a Service (TIaaS) | ||||
| Monitoring Galaxy and Pulsar with Sentry | ||||
15:00 - 15:30 |
Break |
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| Galaxy Interactive Tools | ||||
| Deploying a Beacon v1 in Galaxy | ||||
17:00 |
Wrap Up and Close |
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Friday
We made it! Today we have some additional topics, some of which are not admin related. Please feel free to leave at any point in the day and go enjoy Ghent if the topics are maybe a bit less interesting for you.
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
09:30 - 10:00 |
Welcome and Recap |
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Galaxy Troubleshooting
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11:30 - 11:45 |
Break |
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Tool development and integration into Galaxy
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| Using dataset collections | ||||
| Rule Based Uploader | ||||
13:00 - 14:00 |
Lunch |
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|
Creating a new tutorial
|
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15:00 - 15:30 |
Break |
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17:00 |
Wrap Up and Close |
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Get set up for the course!
Follow the steps below to get set up with everything you need to participate in the course!
Prepare for the Course
Please review the following prerequisites carefully before registering. If you arrive without meeting the prerequisites then the workshop will be a frustrating experience.
Comfortable with the Unix/Linux command line
Most of the workshop will happen at the Linux command line. If you aren’t comfortable with this before you arrive, then you will be lost the entire time. How comfortable do you need to be? Here’s a sampling of commands and concepts that you should be comfortable with:
cd, mkdir, rmdir, ls, tar, gzip, cp, mv, rm, chmod, chown, ln, cat, tail, less, man, grep
~, .., ./, /tmp, |
Note: This is not an exhaustive list (or even a proper subset) of the commands that will be used in the workshop. They are included here to give you an idea of the depth of knowledge that is required.
We have a few tutorials that can help you get refreshed if you need:
Competent in a Unix/Linux text editor
Linux has several text editors available in it. You’ll need to be comfortable in at least one of them before the workshop starts. We recommend that you use Nano, if you don’t know another text editor. It’s simple and easy to use. If you know another editor like Emacs or VIM you are of course welcome to use those as well.
Experience with Linux Package Management
You don’t need to be an expert at Linux package management, but you do need to have some experience at installing and upgrading packages on a Linux system. We’ll be using Ubuntu based images during the workshop, which means we’ll be using apt to do package management. Get to know it. Prerequisites include all of the Introduction Session prerequisites, plus familiarity with the topics presented in that session.
Laptop Requirements
All participants should bring a wifi-enabled laptop with
- Software to access the command line of a Linux server.
- If you are running Linux or Mac OS, then you already have this.
- If you are running Windows than you’ll need to get something like putty installed before the workshop.
- A recent version of either the Firefox or Chrome web browser installed.
Instructor Zone
Check out our checklists for
- Organising a Workshop to check that you haven't forgotten any important step.
- Running a Workshop, helpful reminders closer to your event.
Request TIaaS
Training Infrastructure as a Service (TIaaS) is a service that allows you to request space for your course on a server, it helps ensure courses run smoothly by separating your trainee's jobs into a separate queue. Learn more about TIaaS in our tutorial.
The following links will open a (mostly) pre-filled out TIaaS form,
Once you receive a URL from the admins, please set it as a tiaas_link in your event metadata.
Add your event to the Galaxy Hub Event Horizon
To also list your event on the Galaxy Event Horizon, copy the text below, and add your event to the Galaxy Hub GitHub Repo. Create a folder for your event here, and add an index.md file with the following contents:
---
title: "2025 Galaxy Admin Training (Brno)"
date: '2025-11-24'
days: 5
tease: The ins and outs of setting up your own production quality Galaxy server
#continent: EU
location: "Centrum Šumavská - CESNET,Brno"
external_url: "https://training.galaxyproject.org/training-material/events/2025-11-24-gat-brno.html"
gtn: true
contact: "galaxy@cesnet.cz"
subsites: [all]
---
Promote the Event
Tootable/Tweetable version:
2025 Galaxy Admin Training (Brno)! 📢
The ins and outs of setting up your own production quality Galaxy server
📅 November 24 – 28, 2025
➡️ https://training.galaxyproject.org/training-material/events/2025-11-24-gat-brno.html
📝 Registration is open until 2025-10-01! https://forms.gle/jscWXcYJ7HQLmHoU9
Slack-compatible version:
2025 Galaxy Admin Training (Brno)! 📢
The ins and outs of setting up your own production quality Galaxy server
:calendar: November 24 – 28, 2025
:arrow_right: https://training.galaxyproject.org/training-material/events/2025-11-24-gat-brno.html
:pencil: Registration is open until 2025-10-01! https://forms.gle/jscWXcYJ7HQLmHoU9
Version with schedule:
2025 Galaxy Admin Training (Brno)! 📢
The ins and outs of setting up your own production quality Galaxy server
**Agenda**:
- Monday: Setting up Galaxy with Ansible
- Tuesday: Making the server useful
- Wednesday: Clusters
- Thursday: Expanding
- Friday
📅 November 24 – 28, 2025
➡️ https://training.galaxyproject.org/training-material/events/2025-11-24-gat-brno.html
📝 Registration is open until 2025-10-01! https://forms.gle/jscWXcYJ7HQLmHoU9
Register Now!
Deadline: 1 October 2025
Event details
| event-date | November 24 – 28, 2025 |
| event-location | Centrum Šumavská - CESNET, Šumavská 416, Brno, Czechia, 60200 |
| event-cost | free |
| galaxy@cesnet.cz |
Add this event to your calendar Google Outlook Office 365
Organisers
Martin Čech
Instructors
Marius van den Beek
Björn Grüning
Mira Kuntz
Martin Čech
Martin Demko
In collaboration with
ELIXIR Europe