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.


The European Galaxy Team is hiring!

The Freiburg Galaxy Team is looking for a Systems Engineer/DevOps Engineer!

New Paper "Creating a good learning and sharing environment for bioinformatics"

Tomas Klingström and J.I. Ohlsson have published a paper about the use of BioContainers, Galaxy, and the GTN for bioinformatics researchers.

GCC2022: Registration open for Webinar mode

For those that won't attend in person, the GCC Organizing Committee is happy to announce a virtual webinar-like option

Training Infrastructure Feedback from Hans-Rudolf Hotz and Lucille Delisle

After 2 years running the SIB "Galaxy Introduction for Life Scientists" course only online, we were super happy to stand in front of a crowd and meet again the students in person.

Towards a sustainable storage, enabling co-financing of public infrastructure

Research groups and networks can include their own storage into the European Galaxy server and decide about quota and data policies.


Oct 3 - Oct 7European Galaxy Days (EGD)

European Galaxy Community meeting in Autumn

Oct 3 - Oct 7Cloud Computing Workshop

Online video tutorials about the use of cloud computing resources for MS-based proteomics.

Oct 13Galaxy Community Call: Muon Science community

A forum to share updates and discuss community-wide topics

Oct 27Galaxy Community Call: Galaxy Release Process: Overview and Coming Changes

A forum to share updates and discuss community-wide topics