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

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Contributors

This material was contributed to by:

orcid logoArmin Dadras avatar Armin DadrasCharles Overbeck avatar Charles OverbeckElizabeth Sheets avatar Elizabeth Sheetsorcid logoHelena Rasche avatar Helena Rascheorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoClea Siguret avatar Clea SiguretMiguel Roncoroni avatar Miguel RoncoroniAysam Guerler avatar Aysam Guerlerorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoNadia Goué avatar Nadia Gouéorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDave Clements avatar Dave ClementsWilliam Durand avatar William Durandorcid logoWendi Bacon avatar Wendi Baconorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMaria Doyle avatar Maria Doyleorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAvani Khadilkar avatar Avani Khadilkarorcid logoLisanna Paladin avatar Lisanna PaladinAnne Pajon avatar Anne Pajonorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNate Coraor avatar Nate Coraororcid logoTeresa Müller avatar Teresa MüllerRita Gautschy avatar Rita Gautschyorcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin Čechorcid logoBert Droesbeke avatar Bert DroesbekeAnton Nekrutenko avatar Anton Nekrutenkoorcid logoToby Hodges avatar Toby HodgesDaniela Butano avatar Daniela Butanoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoAnup Kumar avatar Anup KumarBartosz Walkowicz avatar Bartosz WalkowiczSimon Bray avatar Simon BrayYo Yehudi avatar Yo Yehudiorcid logoSimon Gladman avatar Simon Gladmanorcid logoDeepti Varshney avatar Deepti VarshneyEnis Afgan avatar Enis AfganNiall Beard avatar Niall BeardNic Herndon avatar Nic Herndonorcid logoDaniela Schneider avatar Daniela SchneiderEkaterina Polkh avatar Ekaterina Polkhorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLucille Delisle avatar Lucille DelisleMateusz Kuzak avatar Mateusz Kuzakorcid logoPavankumar Videm avatar Pavankumar VidemBoris Depoortere avatar Boris DepoortereGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMarius van den Beek avatar Marius van den Beekorcid logoLaila Los avatar Laila Losorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoSaskia Hiltemann avatar Saskia HiltemannAdelaide Rhodes avatar Adelaide Rhodesorcid logoBérénice Batut avatar Bérénice Batutorcid logoJohn Chilton avatar John Chiltonorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanJon Trow avatar Jon Trow

Funding

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