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
Annotate, prepare tests and publish Galaxy workflows in workflow registries
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

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Contributors

This material was contributed to by:

orcid logoMaria Doyle avatar Maria Doyleorcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony BretaudeauEnis Afgan avatar Enis Afganorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLucille Delisle avatar Lucille DelisleAdelaide Rhodes avatar Adelaide Rhodesorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoDelphine Lariviere avatar Delphine LariviereBartosz Walkowicz avatar Bartosz Walkowiczorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanAnne Pajon avatar Anne PajonBoris Depoortere avatar Boris DepoortereElizabeth Sheets avatar Elizabeth Sheetsorcid logoJohn Chilton avatar John ChiltonAysam Guerler avatar Aysam Guerlerorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoArmin Dadras avatar Armin Dadrasorcid logoNicola Soranzo avatar Nicola SoranzoYo Yehudi avatar Yo YehudiWilliam Durand avatar William Durandorcid logoWendi Bacon avatar Wendi BaconMateusz Kuzak avatar Mateusz KuzakEkaterina Polkh avatar Ekaterina PolkhDaniela Butano avatar Daniela Butanoorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoWolfgang Maier avatar Wolfgang MaierNiall Beard avatar Niall BeardAvani Khadilkar avatar Avani KhadilkarCharles Overbeck avatar Charles Overbeckorcid logoToby Hodges avatar Toby Hodgesorcid logoDave Clements avatar Dave Clementsorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoLaila Los avatar Laila Losorcid logoBérénice Batut avatar Bérénice BatutMiguel Roncoroni avatar Miguel Roncoroniorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNadia Goué avatar Nadia GouéMarius van den Beek avatar Marius van den Beekorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMartin Čech avatar Martin Čechorcid logoTeresa Müller avatar Teresa Müllerorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton NekrutenkoJon Trow avatar Jon TrowNic Herndon avatar Nic Herndonorcid logoNate Coraor avatar Nate Coraororcid logoYvan Le Bras avatar Yvan Le BrasGildas Le Corguillé avatar Gildas Le CorguilléSimon Bray avatar Simon Brayorcid logoClea Siguret avatar Clea Siguretorcid logoBjörn Grüning avatar Björn Grüning

Funding

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