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.

Material

Core

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

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

R

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

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances

Bash

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

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances

SQL

These lessons focus on using learning to write SQL

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances

Other


Assorted other tutorials

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

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 quay.io/galaxy/introduction-training

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.

Maintainers

This material is maintained by:

AvatarJennifer Hillman-JacksonAvatarDave Clements

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

Contributors

This material was contributed to by:

Andrea BagnacaniBérénice BatutSaskia HiltemannAnne PajonNicola SoranzoHelena RascheChristopher BarnettMichele MaroniAnne FouillouxNadia GouéOlha NahornaDave ClementsAnna SymeClemens BlankBjörn GrüningDilmurat YusufSarah PeterAnton NekrutenkoMelanie FöllJoachim WolffCristóbal GallardoMarius van den BeekDaniel BlankenbergAnthony Bretaudeau