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

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 logoMaria Doyle avatar Maria Doyleorcid logoBjörn Grüning avatar Björn GrüningAnne Pajon avatar Anne Pajonorcid logoLucille Delisle avatar Lucille Delisleorcid logoSimon Gladman avatar Simon Gladmanorcid logoToby Hodges avatar Toby HodgesAvani Khadilkar avatar Avani KhadilkarNiall Beard avatar Niall BeardWilliam Durand avatar William Durandorcid logoWendi Bacon avatar Wendi Baconorcid logoNadia Goué avatar Nadia GouéBartosz Walkowicz avatar Bartosz Walkowiczorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoJohn Chilton avatar John Chiltonorcid logoDave Clements avatar Dave ClementsSimon Bray avatar Simon Brayorcid logoHelena Rasche avatar Helena Rascheorcid logoClea Siguret avatar Clea Siguretorcid logoYvan Le Bras avatar Yvan Le BrasElizabeth Sheets avatar Elizabeth Sheetsorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBérénice Batut avatar Bérénice Batutorcid logoDeepti Varshney avatar Deepti VarshneyJon Trow avatar Jon TrowCharles Overbeck avatar Charles OverbeckAysam Guerler avatar Aysam GuerlerMiguel Roncoroni avatar Miguel Roncoroniorcid logoMartin Čech avatar Martin Čechorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoLaila Los avatar Laila LosDaniela Butano avatar Daniela ButanoMarius van den Beek avatar Marius van den Beekorcid logoNate Coraor avatar Nate Coraororcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoBert Droesbeke avatar Bert DroesbekeMateusz Kuzak avatar Mateusz KuzakAnton Nekrutenko avatar Anton NekrutenkoAdelaide Rhodes avatar Adelaide RhodesBoris Depoortere avatar Boris Depoortereorcid logoArmin Dadras avatar Armin Dadrasorcid logoAnthony Bretaudeau avatar Anthony BretaudeauEnis Afgan avatar Enis Afganorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoTeresa Müller avatar Teresa Müllerorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDaniela Schneider avatar Daniela SchneiderNic Herndon avatar Nic HerndonEkaterina Polkh avatar Ekaterina PolkhYo Yehudi avatar Yo Yehudi

Funding

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