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
Introduction to the Dataverse Integration in Galaxy
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
Accessing IIIF from within Galaxy
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

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoArmin Dadras avatar Armin DadrasDaniela Butano avatar Daniela Butanoorcid logoHelena Rasche avatar Helena RascheAnne Pajon avatar Anne PajonSimon Bray avatar Simon Brayorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola SoranzoJon Trow avatar Jon TrowMateusz Kuzak avatar Mateusz KuzakYo Yehudi avatar Yo Yehudiorcid logoMaria Doyle avatar Maria Doyleorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoDeepti Varshney avatar Deepti VarshneyCharles Overbeck avatar Charles OverbeckAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNadia Goué avatar Nadia Gouéorcid logoBjörn Grüning avatar Björn Grüningorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanAysam Guerler avatar Aysam Guerlerorcid logoClea Siguret avatar Clea Siguretorcid logoMarius van den Beek avatar Marius van den BeekRita Gautschy avatar Rita Gautschyorcid logoCristóbal Gallardo avatar Cristóbal GallardoAdelaide Rhodes avatar Adelaide RhodesAvani Khadilkar avatar Avani Khadilkarorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoAnup Kumar avatar Anup Kumarorcid logoWendi Bacon avatar Wendi Baconorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoPavankumar Videm avatar Pavankumar VidemNiall Beard avatar Niall Beardorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoNate Coraor avatar Nate Coraororcid logoDaniela Schneider avatar Daniela SchneiderGildas Le Corguillé avatar Gildas Le Corguilléorcid logoJohn Chilton avatar John Chiltonorcid logoToby Hodges avatar Toby Hodgesorcid logoLisanna Paladin avatar Lisanna PaladinElizabeth Sheets avatar Elizabeth SheetsMiguel Roncoroni avatar Miguel RoncoroniEnis Afgan avatar Enis Afganorcid logoLucille Delisle avatar Lucille DelisleBoris Depoortere avatar Boris Depoortereorcid logoDave Clements avatar Dave Clementsorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa MüllerBartosz Walkowicz avatar Bartosz Walkowiczorcid logoSimon Gladman avatar Simon Gladmanorcid logoMartin Čech avatar Martin ČechNic Herndon avatar Nic Herndonorcid logoLaila Los avatar Laila LosEkaterina Polkh avatar Ekaterina PolkhWilliam Durand avatar William Durandorcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

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