galaxy

About Galaxy

Galaxy is a web-based platform to develeop and execute bioinformatics workflows. Galaxy has extensive online documentation, a good place to get started is the Galaxy 101

Training material and documentation

• training material
• documentation

Community-developed workflows in Galaxy

Most workflows can be found on one of the large Galaxy instances:

• usegalaxy.org
• usegalaxy.eu
• usegalaxy.org.au
• usegalaxy.be
• usegalaxy.fr

A newer initiative exists that publishes best-practice production workflows to Dockstore and WorkflowHub to facilitate Workflow discovery across different Galaxy instances.

Running the minimal proof-of-concept RNA-Seq Galaxy pipeline

1. Register or login to your account on any Galaxy server, e.g usegalaxy.org
2. Open the proof-of-concept workflow on Dockstore
3. Click on the "Launch with Galaxy" button and select a Galaxy server.
4. Click on the workflow version you would like to import
5. Click on the "Run Workflow" button
6. Upload or provide a URL to the input data and run the pipeline using the GUI. Further details on uploading files here

Notes and Contribution

This pipeline is a minimal example of using Galaxy. We welcome contributions to the documentation and workflow, please create an issue or submit a pull request!

How to cite Galaxy

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update" Nucleic Acids Res. (2018) 46(W1):W537-W544 doi:10.1093/nar/gky379

see also https://galaxyproject.org/citing-galaxy/ for more ways to cite Galaxy.