2023 Galaxy Admin Training (Ghent)

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 review the 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, ln
~, .., ./, /tmp,
cat, tail, less
man

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. Organizers will make sure that these editors are available on the Linux images we use in the workshop:

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.

Some 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

  • (Optional but useful) 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.

Registration

Please apply via our form. We only have limited space so please register as soon as possible. If you would like to attend but have funding problems we can support up to 3 people from Low and Middle Income Countries. Please indicate this in the form or contact us directly.

Please feel free to contact us at contact@usegalaxy.eu if you have any question and check this site for any updates.

Logistics

Venue and Accommodation

The Admin training will be held at: Monasterium PoortAckere - 56 Oude Houtlei, Ghent 9000, Belgium (map) The venue is in the city centre of Ghent and within walking distance of several historical attractions. The Monasterium PoortAckere is also a hotel. Participants can make their reservations by filling up the hotel’s reservation form and sending it to reservations@historichotelsbelgium.com. The hotel should then confirm the reservation. We have been advised that reservations made using this route can be cancelled free of charge up to 2 weeks before arrival.

Getting to Ghent

By train

The city of Ghent has a page on the subject here. The main station in Ghent is Gent-Sint-Pieters (map). The Belgian railway system is well connected with the European railway system. Transfers are often at Bruxelles-Midi/Brussel-Zuid/Brussels-South, Antwerp, or Lille (France).

The national railway company (SNCB/NMBS) offers an international route planner here.

To reach the venue from Gent-Sint-Pieters station, one can take tram line 1 or 2 towards the city centre. The city of Ghent offers information on public transport here. Taxis are also available right outside of Gent-Sint-Pieters station.

By plane

The city of Ghent has a page on the subject here.

The two main airports are Brussels Airport - BRU (a.k.a. Luchthaven Zaventem, Luchthaven Brussel-Nationaal, Brussel-Nationale Luchthaven, Aéroport de Bruxelles-National) and Brussels South Charleroi Airport - CRL. From Brussels Airport (BRU) it is convenient to take the train. There is a railway station beneath the airport. There, one can take the train to the Gent-Sint-Pieters station. The national railway company (SNCB/NMBS) offers a route planner.

From Brussels South Charleroi Airport (CRL), there is a shuttle bus service operated by Flibco. Route planner here. To reach the venue from Gent-Sint-Pieters station, one can take tram line 1 or 2 towards the city centre. The city of Ghent offers information on public transport here. Taxis are also available right outside of Gent-Sint-Pieters station.

By car

The city of Ghent has a page on the subject here. Be aware that the venue is inside Ghent’s Low Emission Zone (LEZ). You will likely need to register your car before being able to enter the LEZ (info here). The LEZ is enforced with smart cameras and failing to register the vehicle can lead to a fine of €150 per violation. Be aware that parking in Ghent can be cumbersome and expensive. Please check the venue’s page and the city of Ghent page on parking for the available options.

Who is this course for?

Galaxy administrators, or anyone interested in running a Galaxy server

Event Location

Geocoding via Nominatim, Map data from OpenStreetMap

Organisers & Instructors

This event is brought to you by:

Organisers(s) orcid logoBjörn Grüning avatar Björn Grüning
Instructor(s) orcid logoHelena Rasche avatar Helena Rascheorcid logoNate Coraor avatar Nate CoraorCatherine Bromhead avatar Catherine BromheadMarius van den Beek avatar Marius van den Beekorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMira Kuntz avatar Mira KuntzSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulam
Infrastructure University of Freiburg avatar UFRAustralian BioCommons avatar Australian BioCommons

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

09:30 - 10:00

Welcome and Introduction

Galaxy from an administrator's point of view
Ansible

11:30 - 11:45

Break

Galaxy Installation with Ansible

13:00 - 14:00

Lunch

15:00 - 15:30

Break

Server Maintenance: Cleanup, Backup, and Restoration
Advanced customisation of a Galaxy instance

17:00

Wrap Up and Close

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

Performant Uploads with TUS
Reference Data with Data Managers
Reference Data with CVMFS

11:30 - 11:45

Break

Use Apptainer containers for running Galaxy jobs
Galaxy Tool Management with Ephemeris

13:00 - 14:00

Lunch

Data Libraries

15:00 - 15:30

Break

15:00 - 15:30

Break

Scripting Galaxy using the API and BioBlend

17:00

Wrap Up and Close

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

User, Role, Group, Quota, and Authentication managment
Connecting Galaxy to a compute cluster

11:30 - 11:45

Break

Mapping Jobs to Destinations using TPV

13:00 - 14:00

Lunch

Running Jobs on Remote Resources with Pulsar

15:00 - 15:30

Break

17:00

Wrap Up and Close

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

Setting up Celery Workers for Galaxy
Galaxy Monitoring with Reports
Galaxy Monitoring with Telegraf and Grafana

11:30 - 11:45

Break

Galaxy Monitoring with gxadmin

13:00 - 14:00

Lunch

Training Infrastructure as a Service (TIaaS)
Monitoring Galaxy and Pulsar with Sentry

15:00 - 15:30

Break

Galaxy Interactive Tools
Deploying a Beacon v1 in Galaxy

17:00

Wrap Up and Close

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

Galaxy Troubleshooting

11:30 - 11:45

Break

Tool development and integration into Galaxy
Multisample Analysis
Rule Based Uploader

13:00 - 14:00

Lunch

Creating a new tutorial

15:00 - 15:30

Break

17:00

Wrap Up and Close

Get set up for the course!

Follow the steps below to get set up with everything you need to participate in the course!

Galaxy logo
Create a Galaxy Account

Create an account on one of the following Galaxy servers:

You will get an email with activation link. It may end up in your junk folder.

Note: If you already have a Galaxy account you can skip this step and just log in to your existing account.

Galaxy logo
Prepare for the Course

Please review the 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, ln
~, .., ./, /tmp,
cat, tail, less
man

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. Organizers will make sure that these editors are available on the Linux images we use in the workshop:

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.

Instructor Zone

Check out our checklists for

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, if that server supports TIaaS. Otherwise you might see "page not found".

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: "2023 Galaxy Admin Training (Ghent)"
date: '2023-04-17'
days: 5
tease: The ins and outs of setting up your own production quality Galaxy server
#continent: EU
location: "Monasterium PoortAckere,Ghent"
external_url: "https://training.galaxyproject.org/training-material/events/2023-04-17-gat-gent.html"
gtn: true
contact: "contact@usegalaxy.eu"
subsites: [all]
---

Promote the Event

Tootable/Tweetable version:


2023 Galaxy Admin Training (Ghent)! 📢

The ins and outs of setting up your own production quality Galaxy server

📅 April 17 – 21, 2023
➡️ https://gxy.io/GTN:E00002
📝 Registration is open until 2022-03-01! https://docs.google.com/forms/d/e/1FAIpQLSc3zgDTfcLZ2-92EdgJvfR4j0KxQeOv0tiFMzGXZ6hdW7JlwQ/viewform

Slack-compatible version:


2023 Galaxy Admin Training (Ghent)! 📢

The ins and outs of setting up your own production quality Galaxy server

:calendar: April 17 – 21, 2023
:arrow_right: https://gxy.io/GTN:E00002
:pencil: Registration is open until 2022-03-01! https://docs.google.com/forms/d/e/1FAIpQLSc3zgDTfcLZ2-92EdgJvfR4j0KxQeOv0tiFMzGXZ6hdW7JlwQ/viewform

Version with schedule:


2023 Galaxy Admin Training (Ghent)! 📢

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

📅 April 17 – 21, 2023
➡️ https://gxy.io/GTN:E00002
📝 Registration is open until 2022-03-01! https://docs.google.com/forms/d/e/1FAIpQLSc3zgDTfcLZ2-92EdgJvfR4j0KxQeOv0tiFMzGXZ6hdW7JlwQ/viewform