2023 Galaxy Admin Training (Ghent)

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:

• CLI Basics
• CLI Advanced

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?

Event Location

Geocoding via Nominatim, Map data from OpenStreetMap

Organisers & Instructors

This event is brought to you by:

Organisers(s)	Björn Grüning
Instructor(s)	Helena Rasche Nate Coraor Catherine Bromhead Marius van den Beek Nicola Soranzo Mira Kuntz Sanjay Kumar Srikakulam
Infrastructure	UFR Australian BioCommons

EOSC-Life

EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087

EuroScienceGateway

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.

ELIXIR Europe