Galaxy tool wrapping hackathon

Date: 11th December 2026
Time: 10:00–16:30
Location: SURF, Science Park 140, 1098 XG Amsterdam
Format: In person
Sign-up: https://forms.gle/Z6cG5zkqQk7E6KqJ9

Make your command-line tool usable by thousands of researchers - without them ever touching a terminal!

During the event, participants will learn how to wrap their tools inside Galaxy, test it with Planemo, and open a pull request to the tools repository. 

This event is organised by SURF within the NWO TDCC-LSH project "FAIR tool framework".

Draft agenda:

9:30 - 10:00 Welcome
10:00 - 11:00 Introduction to Galaxy
11:00 - 12:15 Getting started with Planemo
12:15 - 13:00 Lunch
13:00 - 14:15 Hackathon part 1
14:15 - 14:45 Coffee break
14:45 - 16:00 Hackathon part 2
16:00 - 16:30 Closing

Maximum capacity: 16 participants. Tools made by Dutch developers and participants affiliated with Dutch institutes will have priority.

Hackathon requirements:

• It runs non-interactively from the command line: one command, no prompts and no GUI. (Note: Galaxy also supports the so-called interactive tools. However, this will not be covered in this session)
• Its inputs and outputs use file formats Galaxy already supports (see https://usegalaxy.org/datatypes).
• It is installable via conda — ideally already available on Bioconda.
• It has an open-source licence that allows redistribution.
• It has not already been wrapped for Galaxy — please check the Galaxy Tool Shed and the tools-iuc repository. Updating an outdated existing wrapper is also a welcome project.
• The tool runs on Linux (Ubuntu 24).

Requirements for the participants:

• Comfortable working in a Linux terminal: editing files, running commands, reading error messages.
• Basic Git: clone, commit, push.
• Familiar with the tool's command-line options and typical use, as its developer or as an experienced user.
• Your own laptop with a web browser and an SSH client.

Before the event:

• Create a GitHub account and set up an SSH key or personal access token.
• Prepare a small test input (< 1 MB) for your tool and the output it should produce. You can also check the tests from the original repository
• New to Galaxy? Follow the Galaxy Training Network tutorial "A short introduction to Galaxy".
• Make sure you have access to SURF Research Cloud. Two days prior to the hackathon, access will be given to the SRC environment.

New to SRC? Join one of the introductory trainings:

November 5, Erasmus MC. Register here 

November 10, Tilburg University. Register here 

December 10, Amsterdam UMC. Register here

Registration costs: 

Free of charge.
This hackathon is sponsored by the NWO TDCC-LSH.

Need help?

Contact: Mirela Minkova, mirela.minkova@surf.nl