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.


Evaluation of the current usage and future needs of Galaxy for microbial data analysis - We Need Your Help!

The microGalaxy community of practice would like to learn more about use-cases where Galaxy was beneficial, and also the barriers that prevent researchers from using Galaxy. The aim is to collectively find solutions to improve user experience and reduce barriers. To this end, we are launching a survey to reach out to, and learn from, the microbial research community.

New Paper "Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart"

Siatra et al. have used the European Galaxy server to identify cell populations capable of cardiac regeneration that we will be able to trace and monitor

Effortlessly navigate your Galaxy history with enhanced search options

Data searchability in the Galaxy History panel has been taken to new levels with the advanced search options that allow users to not only find items with more ease, but also find relations within items in their history.

Enjoy a much faster user interface

Following up on our modernization efforts, we now introduce a single top-router written in Vue, which brings all our Vue components together in a seamless user experience, dramatically reducing the number of required page reloads when navigating the Galaxy user interface.

Galaxy Mentor Network: Reset

We launched the Galaxy Mentor Network one year ago with the idea to onboard new members in the community. Now, one year later, we realize that we failed. We still believe in the power that the Galaxy Mentor Network, and, in that spirit, we would like to relaunch the Galaxy Mentor Network with a new matching process.


Apr 19 - Apr 20Imaging in Galaxy

Workshop 'BioImaging and the European Open Science Cloud' organised by Euro-BioImaging ERIC in collaboration with EOSC-Life

May 22 - May 26GTN Smörgåsbord 2023

We are happy to announce that the next edition of the GTN Smörgåsbord training event will take place on May 22-26, 2023! It will once again be free, online, self-paced, and choose-your-own-adventure style. It will feature all the content of previous editions, plus lots more!

Mar 30Galaxy Metabolomics Community Call

A forum to share updates and discuss community-wide topics.

Apr 13Galaxy Community Call: AnVIL Project

A forum to share updates and discuss community-wide topics

May 4Galaxy Community Call: Galaxy for Cancer

A forum to share updates and discuss community-wide topics