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
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:

orcid logoWolfgang Maier avatar Wolfgang Maierorcid logoYvan Le Bras avatar Yvan Le BrasMateusz Kuzak avatar Mateusz Kuzakorcid logoNate Coraor avatar Nate Coraororcid logoSimon Gladman avatar Simon GladmanBoris Depoortere avatar Boris DepoortereNic Herndon avatar Nic Herndonorcid logoWendi Bacon avatar Wendi BaconWilliam Durand avatar William DurandBartosz Walkowicz avatar Bartosz Walkowiczorcid logoArmin Dadras avatar Armin Dadrasorcid logoBérénice Batut avatar Bérénice BatutSimon Bray avatar Simon Brayorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia HiltemannAdelaide Rhodes avatar Adelaide Rhodesorcid logoMartin Čech avatar Martin ČechMiguel Roncoroni avatar Miguel Roncoroniorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoŁukasz Opioła avatar Łukasz OpiołaAysam Guerler avatar Aysam GuerlerAnton Nekrutenko avatar Anton NekrutenkoAnne Pajon avatar Anne Pajonorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoJohn Chilton avatar John Chiltonorcid logoMaria Doyle avatar Maria DoyleJon Trow avatar Jon Troworcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBjörn Grüning avatar Björn Grüningorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanEnis Afgan avatar Enis AfganEkaterina Polkh avatar Ekaterina PolkhAvani Khadilkar avatar Avani Khadilkarorcid logoDelphine Lariviere avatar Delphine LariviereElizabeth Sheets avatar Elizabeth Sheetsorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosCharles Overbeck avatar Charles Overbeckorcid logoHelena Rasche avatar Helena Rascheorcid logoToby Hodges avatar Toby Hodgesorcid logoLucille Delisle avatar Lucille Delisleorcid logoDave Clements avatar Dave ClementsDaniela Butano avatar Daniela Butanoorcid logoDeepti Varshney avatar Deepti VarshneyNiall Beard avatar Niall Beardorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoLaila Los avatar Laila Losorcid logoTeresa Müller avatar Teresa MüllerYo Yehudi avatar Yo YehudiMarius van den Beek avatar Marius van den Beekorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Funding

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