How to use Galaxy?


In the left panel of this page you will find the list of available tools, you can see this page at any point by clicking 'Analyze Data' in the top menu.


The history of your current data analysis is shown in the right panel. A good practice when running multiple analysis in parallel is to create several histories and give each one a unique name. You can click on 'View all histories' button (upper right corner in histories panel) to get an overview and switch between the current histories.

Input Data

Every analysis starts with getting the input data into your current history (right panel). To do this you can upload your own input files or use shared datasets. To upload files from your computer or instruct Galaxy to download files from the web you have to use of the upload tool: Get data (tool panel on the left) → upload file. Please DO NOT UPLOAD LARGE FILES (~GB), but contact the administrator to create a central data repository! To use available shared data you have to click on Shared data (top menu) → Data Libraries. You can then browse the available libraries and select the file/s you want to use. By clicking 'to History' button and choosing the desired History name you will import these files and make them available to use as input for future analysis.


To run a job select the tool from tool panel on the left, then the corresponding interface will be loaded and you will be able to select corresponding input data and (re)define parameters. Please read carefully the labels and help text next to the input fields. After clicking Execute you will be able to see entries for each in your history. The color of a dataset designates the current status of the underlying job

Color State
Gray The job is being evaluated to run (new dataset) or is queued. Allow this to complete.
Yellow The job is executing.
Green Successful processing.
Red The job has failed.
Blue The job is paused. This indicates either a problem with an input (a previous step in the workflow may have failed) or that you have exceeded disk quota set by the administrator of the Galaxy instance you are working on.


You can automate your analysis pipeline by using workflows composed of several tools linked by their input/output data. In the Workflows section (upper menu) you can see a list of current workflows and also create your own ones. It is also possible (and highly recommended) to use the shared, and widely tested, workflows available under Shared Data (top menu) → workflows. To use one of these you first need to import it to your workflows list by clicking on the name and selecting Import. To execute any workflow listed under your workflows first click on it and select run, then choose the input data as with any tool.


Stronger together: first FAIR-EASE and EuroScienceGateway workshop

Presenting some outcomes from the first joined FAIR-EASE / EuroScienceGateway workshop

New Paper "A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature"

Sabbaghian and colleagues have used the European Galaxy server to study miRNAs as biomarkers for cancer

New Galaxy training: Genome-wide alternative splicing analysis

GTN hosts a new training for analyzing alternative splicing at genome-wide scale

Replacing the Job Router with Zero Downtime on EU

Mothballing the Sorting Hat – how we migrated our dynamic job routing

Galaxy taking part @ Applied Bioinformatics & Public Health Microbiology 2023

From the 3rd to the 5th of May, Engy Nasr from the Freiburg Galaxy team travelled to Hinxton, England to join and present her work at the Applied Bioinformatics & Public Health Microbiology 2023 conference


Jun 12 - Jun 15Gallantries & ELIXIR-GOBLET Train the Trainers

This course introduces trainers to learning principles, training techniques, lesson, session, course, and material design as well as assessment and feedback. This course is has been developed for by trainers in the bioinformatics but is suitable for all trainers and educators in higher education.

Jun 15Galaxy Community Call

A forum to share updates and discuss community-wide topics

Jul 6Galaxy Community Call

A forum to share updates and discuss community-wide topics

Jul 10 - Jul 162023 Galaxy Community Conference (GCC2023)

The annual gathering of the Galaxy Community with opportunities to hear latest developments, get training, and meet everyone involved.

Jul 14 - Jul 18International Congress of Genetics

Meeting once every 5 years, and right on the heels of GCC2023 in a nearby location, come and check out this year's conference theme: Genetics and Genomics - Linking Life and Society.