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:

Anne Pajon avatar Anne PajonBartosz Walkowicz avatar Bartosz Walkowiczorcid logoNate Coraor avatar Nate CoraorCharles Overbeck avatar Charles Overbeckorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanYo Yehudi avatar Yo Yehudiorcid logoJohn Chilton avatar John ChiltonMiguel Roncoroni avatar Miguel Roncoroniorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMaria Doyle avatar Maria Doyleorcid logoSimon Gladman avatar Simon GladmanNic Herndon avatar Nic Herndonorcid logoNadia Goué avatar Nadia GouéBoris Depoortere avatar Boris Depoortereorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoBjörn Grüning avatar Björn GrüningWilliam Durand avatar William Durandorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola SoranzoDaniela Butano avatar Daniela ButanoMateusz Kuzak avatar Mateusz Kuzakorcid logoLisanna Paladin avatar Lisanna PaladinEkaterina Polkh avatar Ekaterina Polkhorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBérénice Batut avatar Bérénice Batutorcid logoArmin Dadras avatar Armin DadrasElizabeth Sheets avatar Elizabeth SheetsAysam Guerler avatar Aysam Guerlerorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoToby Hodges avatar Toby Hodgesorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDaniela Schneider avatar Daniela SchneiderMarius van den Beek avatar Marius van den Beekorcid logoDelphine Lariviere avatar Delphine LariviereJon Trow avatar Jon Troworcid logoWolfgang Maier avatar Wolfgang Maierorcid logoWendi Bacon avatar Wendi Baconorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLaila Los avatar Laila LosSimon Bray avatar Simon BrayAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoLucille Delisle avatar Lucille Delisleorcid logoMartin Čech avatar Martin Čechorcid logoClea Siguret avatar Clea Siguretorcid logoYvan Le Bras avatar Yvan Le BrasNiall Beard avatar Niall Beardorcid logoDave Clements avatar Dave ClementsEnis Afgan avatar Enis Afganorcid logoTeresa Müller avatar Teresa MüllerAvani Khadilkar avatar Avani KhadilkarAdelaide Rhodes avatar Adelaide Rhodes

Funding

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