CoCalc -- 2025-11-24-gat-brno.md

GitHub Repository: galaxyproject/training-material
Path: blob/main/events/2025-11-24-gat-brno.md
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---

layout: event

title: "2025 Galaxy Admin Training (Brno)"
description: "The ins and outs of setting up your own production quality Galaxy server"
location:
  geo:
    lat: 49.212017
    lon: 16.5955944
  name: Centrum Šumavská - CESNET
  address: Šumavská 416
  city: Brno
  country: Czechia
  postcode: "60200"
date_start: 2025-11-24
date_end: 2025-11-28

cover-image: /assets/images/gat-small.png
cover-image-alt: GTN logo on a spiral galaxy background with text galaxy admin training

tags:
- admin

registration:
    link: "https://forms.gle/jscWXcYJ7HQLmHoU9"
    deadline: 2025-10-01
cost: free
async: false
mode: onsite
audience: Galaxy administrators, or anyone interested in running a Galaxy server
contact_email: galaxy@cesnet.cz

contributions:
  organisers: [martenson]
  instructors: [mvdbeek, bgruening, mira-miracoli, martenson, martindemko]
  infrastructure: []
  funding: [elixir-europe]

infrastructure:
  custom:
    description: |
        **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:

        - [CLI Basics](https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-basics/tutorial.html)
        - [CLI Advanced](https://training.galaxyproject.org/training-material/topics/data-science/tutorials/cli-advanced/tutorial.html)

        #### 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](https://www.nano-editor.org/), if you don't know another text editor. It's [simple and easy to use](https://www.howtogeek.com/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/). If you know another editor like [Emacs](https://www.gnu.org/software/emacs/) or [VIM](http://www.vim.org/) 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**](https://help.ubuntu.com/community/AptGet/Howto) 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](https://putty.software/) installed before the workshop.
        - A recent version of either the Firefox or Chrome web browser installed.



program:
  - section: "Monday: Setting up Galaxy with Ansible"
    description: This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.
    tutorials:
      - type: custom
        name: Registration
        time: "09:00 - 09:30"
      - type: custom
        name: Welcome and Introduction
        time: "09:30 - 10:00"
      - name: introduction
        topic: admin
      - name: ansible
        topic: admin
      - type: custom
        name: Break
        time: "11:30 - 11:45"
      - name: ansible-galaxy
        topic: admin
      - type: custom
        name: Lunch
        time: "13:00 - 14:00"
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      - name: backup-cleanup
        topic: admin
      - name: advanced-galaxy-customisation
        topic: admin
      - type: custom
        name: Wrap Up and Close
        time: "17:00"

  - section: "Tuesday: Making the server useful"
    description: |
        Today we pivot to focus on making that server useful: adding tools and
        data, configuring quotas, etc.
    tutorials:
      - type: custom
        name: Welcome and Recap
        time: "09:30 - 10:00"
      - name: tus
        topic: admin
      - name: reference-genomes
        topic: admin
      - name: cvmfs
        topic: admin
      - type: custom
        name: Break
        time: "11:30 - 11:45"

      - name: apptainer
        topic: admin
      - name: tool-management
        topic: admin

      - type: custom
        name: Lunch
        time: "13:00 - 14:00"
      - name: data-library
        topic: admin
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      #- name: users-groups-quotas
      #  topic: admin
      - name: bioblend-api
        topic: dev
      - type: custom
        name: Wrap Up and Close
        time: "17:00"

  - section: "Wednesday: Clusters"
    description: |
        Today we focus on connecting the Galaxy server to a compute cluster,
        and explore job configuration and TPV
    tutorials:
      - type: custom
        name: Welcome and Recap
        time: "09:30 - 10:00"
      - name: users-groups-quotas
        topic: admin
      - name: connect-to-compute-cluster
        topic: admin
      - type: custom
        name: Break
        time: "11:30 - 11:45"
      - name: job-destinations
        topic: admin
      - type: custom
        name: Lunch
        time: "13:00 - 14:00"
      - name: pulsar
        topic: admin
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      - type: custom
        name: Wrap Up and Close
        time: "17:00"

  - section: "Thursday: Expanding"
    description: |
        Today we focus on running jobs on remote resources, then look into
        monitoring, data uploads, etc.
    tutorials:
      - type: custom
        name: Welcome and Recap
        time: "09:30 - 10:00"
      - name: celery
        topic: admin
      - name: reports
        topic: admin
      - name: monitoring
        topic: admin
      - type: custom
        name: Break
        time: "11:30 - 11:45"
      - name: gxadmin
        topic: admin
      - type: custom
        name: Lunch
        time: "13:00 - 14:00"
      - name: tiaas
        topic: admin
      - name: sentry
        topic: admin
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      - name: interactive-tools
        topic: admin
      - name: beacon
        topic: admin
      - type: custom
        name: Wrap Up and Close
        time: "17:00"

  - section: "Friday"
    description: |
        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.
    tutorials:
      - type: custom
        name: Welcome and Recap
        time: "09:30 - 10:00"
      - name: troubleshooting
        topic: admin
      - type: custom
        name: Break
        time: "11:30 - 11:45"
      - name: tool-integration
        topic: dev
      - name: collections
        topic: galaxy-interface
      - name: upload-rules
        topic: galaxy-interface
      - type: custom
        name: Lunch
        time: "13:00 - 14:00"
      - name: create-new-tutorial
        topic: contributing
      - type: custom
        name: Break
        time: "15:00 - 15:30"
      - type: custom
        name: Wrap Up and Close
        time: "17:00"

---

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 [email protected] 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).