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:

William Durand avatar William Durandorcid logoArmin Dadras avatar Armin DadrasMarius van den Beek avatar Marius van den BeekBartosz Walkowicz avatar Bartosz WalkowiczSimon Bray avatar Simon BrayBoris Depoortere avatar Boris DepoortereAnne Pajon avatar Anne Pajonorcid logoDave Clements avatar Dave ClementsNic Herndon avatar Nic Herndonorcid logoJohn Chilton avatar John ChiltonCharles Overbeck avatar Charles OverbeckAysam Guerler avatar Aysam Guerlerorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnup Kumar avatar Anup Kumarorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoAnthony Bretaudeau avatar Anthony BretaudeauGildas Le Corguillé avatar Gildas Le CorguilléEkaterina Polkh avatar Ekaterina Polkhorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoMaria Doyle avatar Maria Doyleorcid logoNate Coraor avatar Nate CoraorNiall Beard avatar Niall BeardJon Trow avatar Jon Troworcid logoHelena Rasche avatar Helena Rascheorcid logoDaniela Schneider avatar Daniela SchneiderElizabeth Sheets avatar Elizabeth Sheetsorcid logoLaila Los avatar Laila Losorcid logoMartin Čech avatar Martin Čechorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnne Fouilloux avatar Anne FouillouxMiguel Roncoroni avatar Miguel Roncoroniorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoLisanna Paladin avatar Lisanna PaladinMateusz Kuzak avatar Mateusz Kuzakorcid logoToby Hodges avatar Toby HodgesEnis Afgan avatar Enis AfganDaniela Butano avatar Daniela ButanoAvani Khadilkar avatar Avani Khadilkarorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoLucille Delisle avatar Lucille Delisleorcid logoNadia Goué avatar Nadia Gouéorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoClea Siguret avatar Clea SiguretYo Yehudi avatar Yo Yehudiorcid logoWolfgang Maier avatar Wolfgang MaierRita Gautschy avatar Rita Gautschyorcid logoWendi Bacon avatar Wendi Baconorcid logoTeresa Müller avatar Teresa Müllerorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton NekrutenkoAdelaide Rhodes avatar Adelaide Rhodes

Funding

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