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
Importing (uploading) data from Onedata
Onedata user-owned storage
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
Exporting to Onedata remote

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Getting started with Onedata distributed storage
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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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa Müller

Contributors

This material was contributed to by:

Charles Overbeck avatar Charles OverbeckDaniela Butano avatar Daniela ButanoAvani Khadilkar avatar Avani Khadilkarorcid logoBérénice Batut avatar Bérénice BatutEnis Afgan avatar Enis Afganorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoTeresa Müller avatar Teresa Müllerorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosNic Herndon avatar Nic Herndonorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoŁukasz Opioła avatar Łukasz OpiołaElizabeth Sheets avatar Elizabeth SheetsMateusz Kuzak avatar Mateusz Kuzakorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoDave Clements avatar Dave ClementsMarius van den Beek avatar Marius van den Beekorcid logoNate Coraor avatar Nate CoraorNiall Beard avatar Niall Beardorcid logoJohn Chilton avatar John Chiltonorcid logoDelphine Lariviere avatar Delphine LariviereSimon Bray avatar Simon Brayorcid logoCristóbal Gallardo avatar Cristóbal GallardoWilliam Durand avatar William Durandorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaila Los avatar Laila LosAnne Pajon avatar Anne Pajonorcid logoSimon Gladman avatar Simon Gladmanorcid logoToby Hodges avatar Toby HodgesJon Trow avatar Jon TrowMiguel Roncoroni avatar Miguel Roncoroniorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoWendi Bacon avatar Wendi Baconorcid logoMaria Doyle avatar Maria Doyleorcid logoLucille Delisle avatar Lucille Delisleorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoArmin Dadras avatar Armin DadrasAnton Nekrutenko avatar Anton NekrutenkoBartosz Walkowicz avatar Bartosz WalkowiczBoris Depoortere avatar Boris DepoortereYo Yehudi avatar Yo Yehudiorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMartin Čech avatar Martin Čechorcid logoHelena Rasche avatar Helena Rascheorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanAdelaide Rhodes avatar Adelaide RhodesAysam Guerler avatar Aysam GuerlerEkaterina Polkh avatar Ekaterina Polkhorcid logoBert Droesbeke avatar Bert Droesbeke

Funding

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