Using Galaxy and Managing your Data

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

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

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

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
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.

Follow topic updates rss-feed with our RSS Feed

Community Resources

Community Home Maintainer Home

Editorial Board

This material is reviewed by our Editorial Board:

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

Contributors

This material was contributed to by:

Mateusz Kuzak avatar Mateusz KuzakTeresa Müller avatar Teresa Müllerorcid logoDave Clements avatar Dave Clementsorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBjörn Grüning avatar Björn GrüningEkaterina Polkh avatar Ekaterina PolkhWilliam Durand avatar William Durandorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoYvan Le Bras avatar Yvan Le BrasAvani Khadilkar avatar Avani Khadilkarorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoArmin Dadras avatar Armin DadrasSimon Bray avatar Simon BrayAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria DoyleEnis Afgan avatar Enis AfganNiall Beard avatar Niall BeardYo Yehudi avatar Yo Yehudiorcid logoMartin Čech avatar Martin Čechorcid logoSimon Gladman avatar Simon GladmanNic Herndon avatar Nic Herndonorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLaila Los avatar Laila LosElizabeth Sheets avatar Elizabeth SheetsAnne Pajon avatar Anne PajonMarius van den Beek avatar Marius van den BeekJon Trow avatar Jon Troworcid logoNate Coraor avatar Nate CoraorCharles Overbeck avatar Charles Overbeckorcid logoAnthony Bretaudeau avatar Anthony BretaudeauAdelaide Rhodes avatar Adelaide Rhodesorcid logoJohn Chilton avatar John ChiltonAysam Guerler avatar Aysam Guerlerorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoHelena Rasche avatar Helena RascheMiguel Roncoroni avatar Miguel RoncoroniDaniela Butano avatar Daniela ButanoDeepti Varshney avatar Deepti Varshneyorcid logoLucille Delisle avatar Lucille Delisleorcid logoWendi Bacon avatar Wendi Baconorcid logoSaskia Hiltemann avatar Saskia HiltemannBoris Depoortere avatar Boris Depoortereorcid logoToby Hodges avatar Toby Hodgesorcid logoCristóbal Gallardo avatar Cristóbal Gallardo

Funding

These individuals or organisations provided funding support for the development of this resource