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

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Contributors

This material was contributed to by:

Niall Beard avatar Niall BeardEkaterina Polkh avatar Ekaterina Polkhorcid logoSaskia Hiltemann avatar Saskia HiltemannMiguel Roncoroni avatar Miguel Roncoroniorcid logoMartin Čech avatar Martin ČechMateusz Kuzak avatar Mateusz Kuzakorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoTeresa Müller avatar Teresa MüllerAvani Khadilkar avatar Avani KhadilkarEnis Afgan avatar Enis Afganorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton Nekrutenkoorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoAnne Fouilloux avatar Anne FouillouxCharles Overbeck avatar Charles Overbeckorcid logoNate Coraor avatar Nate Coraororcid logoAnthony Bretaudeau avatar Anthony BretaudeauJon Trow avatar Jon TrowMarius van den Beek avatar Marius van den Beekorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosBartosz Walkowicz avatar Bartosz Walkowiczorcid logoBérénice Batut avatar Bérénice Batutorcid logoArmin Dadras avatar Armin Dadrasorcid logoMaria Doyle avatar Maria Doyleorcid logoLisanna Paladin avatar Lisanna PaladinNic Herndon avatar Nic Herndonorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoToby Hodges avatar Toby Hodgesorcid logoJohn Chilton avatar John ChiltonDaniela Butano avatar Daniela Butanoorcid logoClea Siguret avatar Clea Siguretorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoLucille Delisle avatar Lucille DelisleAysam Guerler avatar Aysam Guerlerorcid logoSimon Gladman avatar Simon Gladmanorcid logoWendi Bacon avatar Wendi Baconorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoDaniela Schneider avatar Daniela SchneiderAdelaide Rhodes avatar Adelaide Rhodesorcid logoDave Clements avatar Dave Clementsorcid logoLaila Los avatar Laila LosAnne Pajon avatar Anne PajonBoris Depoortere avatar Boris Depoortereorcid logoYvan Le Bras avatar Yvan Le BrasWilliam Durand avatar William Durandorcid logoHelena Rasche avatar Helena Rascheorcid logoNadia Goué avatar Nadia GouéElizabeth Sheets avatar Elizabeth SheetsSimon Bray avatar Simon BrayYo Yehudi avatar Yo Yehudi

Funding

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