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

Contributors

This material was contributed to by:

orcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosWilliam Durand avatar William DurandAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSimon Gladman avatar Simon Gladmanorcid logoMartin Čech avatar Martin ČechAdelaide Rhodes avatar Adelaide Rhodesorcid logoLisanna Paladin avatar Lisanna PaladinEnis Afgan avatar Enis AfganSimon Bray avatar Simon BrayMiguel Roncoroni avatar Miguel Roncoroniorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanAvani Khadilkar avatar Avani Khadilkarorcid logoJohn Chilton avatar John Chiltonorcid logoBert Droesbeke avatar Bert DroesbekeBoris Depoortere avatar Boris Depoortereorcid logoWendi Bacon avatar Wendi BaconAnne Pajon avatar Anne Pajonorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBérénice Batut avatar Bérénice Batutorcid logoNadia Goué avatar Nadia Gouéorcid logoLaila Los avatar Laila Losorcid logoYvan Le Bras avatar Yvan Le BrasYo Yehudi avatar Yo Yehudiorcid logoAnne Fouilloux avatar Anne FouillouxJon Trow avatar Jon Troworcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTeresa Müller avatar Teresa Müllerorcid logoToby Hodges avatar Toby HodgesElizabeth Sheets avatar Elizabeth Sheetsorcid logoNate Coraor avatar Nate CoraorNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoBjörn Grüning avatar Björn Grüningorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMaria Doyle avatar Maria DoyleEkaterina Polkh avatar Ekaterina PolkhMateusz Kuzak avatar Mateusz KuzakDaniela Butano avatar Daniela Butanoorcid logoHelena Rasche avatar Helena RascheMarius van den Beek avatar Marius van den Beekorcid logoLucille Delisle avatar Lucille DelisleAysam Guerler avatar Aysam Guerlerorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBartosz Walkowicz avatar Bartosz Walkowiczorcid logoClea Siguret avatar Clea Siguretorcid logoDaniela Schneider avatar Daniela SchneiderCharles Overbeck avatar Charles Overbeckorcid logoDave Clements avatar Dave Clementsorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoArmin Dadras avatar Armin DadrasNic Herndon avatar Nic Herndon

Funding

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