Using Galaxy and Managing your Data

A collection of microtutorials explaining various features of the Galaxy user interface and manipulating data within Galaxy.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.


Uploading Data

These tutorials will help you get data into Galaxy, before you analyse it.

Lesson Slides Hands-on Recordings
Getting data into Galaxy
Rule Based Uploader
Rule Based Uploader: Advanced
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis


Managing your analysis histories efficiently

Lesson Slides Hands-on Recordings
Searching Your History
Understanding Galaxy history system

Making Data Manageable

Now that you have data in Galaxy, let's make it easier to work with through collections and structured data.

Lesson Slides Hands-on Recordings
Group tags for complex experimental designs
Multisample Analysis
Name tags for following complex histories
Using dataset collections


Using Galaxy workflows to scale analysis

Lesson Slides Hands-on Recordings
Automating Galaxy workflows using the command line
Creating high resolution images of Galaxy Workflows
Creating, Editing and Importing Galaxy Workflows
Extracting Workflows from Histories
Galaxy workflows in Dockstore
Using Workflow Parameters
Workflow Reports

Analysing Data

Some advanced topics in data analysis.

Lesson Slides Hands-on Recordings
InterMine integration with Galaxy
JupyterLab in Galaxy
RStudio in Galaxy
Use Jupyter notebooks in Galaxy

Download and free up space

Once you are done with your analyses in Galaxy, it's time to download your data and free up space.

Lesson Slides Hands-on Recordings
Downloading and Deleting Data in Galaxy


Assorted Tutorials

Lesson Slides Hands-on Recordings
Submitting sequence data to ENA

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.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoHelena Rasche avatar Helena Rasche

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:

orcid logoMaria Doyle avatar Maria Doyleorcid logoToby Hodges avatar Toby HodgesAysam Guerler avatar Aysam GuerlerAnne Pajon avatar Anne Pajonorcid logoJohn Chilton avatar John Chiltonorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoWolfgang Maier avatar Wolfgang MaierSimon Bray avatar Simon BrayAvani Khadilkar avatar Avani KhadilkarCharles Overbeck avatar Charles OverbeckEkaterina Polkh avatar Ekaterina PolkhEnis Afgan avatar Enis Afganorcid logoSaskia Hiltemann avatar Saskia HiltemannAdelaide Rhodes avatar Adelaide Rhodesorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBérénice Batut avatar Bérénice BatutMiguel Roncoroni avatar Miguel Roncoroniorcid logoBert Droesbeke avatar Bert DroesbekeJon Trow avatar Jon TrowYo Yehudi avatar Yo Yehudiorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton NekrutenkoElizabeth Sheets avatar Elizabeth SheetsMarius van den Beek avatar Marius van den Beekorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave Clementsorcid logoSimon Gladman avatar Simon GladmanBoris Depoortere avatar Boris DepoortereDaniela Butano avatar Daniela Butanoorcid logoLaila Los avatar Laila Losorcid logoMartin Čech avatar Martin Čech


This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries