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.

Material

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

Histories

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

Workflows

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

Other

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.

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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.

Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoHelena Rasche avatar Helena RascheBoris Depoortere avatar Boris DepoortereElizabeth Sheets avatar Elizabeth SheetsAdelaide Rhodes avatar Adelaide Rhodesorcid logoDelphine Lariviere avatar Delphine LariviereAvani Khadilkar avatar Avani KhadilkarEnis Afgan avatar Enis AfganMarius van den Beek avatar Marius van den Beekorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoMaria Doyle avatar Maria Doyleorcid logoDave Clements avatar Dave ClementsEkaterina Polkh avatar Ekaterina Polkhorcid logoAnne Fouilloux avatar Anne FouillouxDaniela Butano avatar Daniela Butanoorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton NekrutenkoYo Yehudi avatar Yo Yehudiorcid logoMartin Čech avatar Martin Čechorcid logoCristóbal Gallardo avatar Cristóbal GallardoMiguel Roncoroni avatar Miguel RoncoroniAysam Guerler avatar Aysam GuerlerCharles Overbeck avatar Charles Overbeckorcid logoJohn Chilton avatar John Chiltonorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLaila Los avatar Laila Losorcid logoSimon Gladman avatar Simon GladmanAnne Pajon avatar Anne PajonJon Trow avatar Jon TrowSimon Bray avatar Simon Brayorcid logoToby Hodges avatar Toby Hodges

Funders

This material was funded by:

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