Introduction to Galaxy Analyses

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.



These are the core, foundational topics for learning how to use Galaxy.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
Introduction to Galaxy
A short introduction to Galaxy
plain text tutorial
From peaks to genes
Galaxy 101
Galaxy 101 for everyone
How to reproduce published Galaxy analyses
Introduction to Genomics and Galaxy
NGS data logistics
Options for using Galaxy
plain text


These lessons focus on coding in R, using Galaxy analysis outputs as their basis.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
Advanced R in Galaxy
R basics in Galaxy


These lessons focus on using the Command Line Interface and Bash for processing data.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour


Assorted other tutorials

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
IGV Introduction

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.


This material is maintained by:

AvatarJennifer Hillman-Jackson AvatarDave Clements

For any question related to this topic and the content, you can contact them or visit our Gitter channel.


This material was contributed to by:

AvatarAndrea Bagnacani AvatarBérénice Batut AvatarSaskia Hiltemann AvatarAnne Pajon AvatarNicola Soranzo AvatarHelena Rasche AvatarChristopher Barnett AvatarMichele Maroni AvatarAnne Fouilloux AvatarNadia Goué AvatarOlha Nahorna AvatarDave Clements AvatarAnna Syme AvatarThe Carpentries AvatarFotis E. Psomopoulos AvatarToby Hodges AvatarClemens Blank AvatarBjörn Grüning AvatarDilmurat Yusuf AvatarSarah Peter AvatarAnton Nekrutenko AvatarMelanie Föll AvatarJoachim Wolff AvatarCristóbal Gallardo AvatarMarius van den Beek AvatarDaniel Blankenberg AvatarAnthony Bretaudeau