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:

Enis Afgan avatar Enis Afganorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoBjörn Grüning avatar Björn Grüningorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoMartin Čech avatar Martin ČechDaniela Butano avatar Daniela ButanoJon Trow avatar Jon Troworcid logoDeepti Varshney avatar Deepti VarshneyAysam Guerler avatar Aysam GuerlerAnne Pajon avatar Anne Pajonorcid logoJohn Chilton avatar John ChiltonNic Herndon avatar Nic HerndonBartosz Walkowicz avatar Bartosz Walkowiczorcid logoTeresa Müller avatar Teresa MüllerWilliam Durand avatar William Durandorcid logoDave Clements avatar Dave ClementsAvani Khadilkar avatar Avani KhadilkarElizabeth Sheets avatar Elizabeth SheetsEkaterina Polkh avatar Ekaterina Polkhorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHelena Rasche avatar Helena Rascheorcid logoLaila Los avatar Laila Losorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoWendi Bacon avatar Wendi BaconCharles Overbeck avatar Charles Overbeckorcid logoNate Coraor avatar Nate Coraororcid logoBérénice Batut avatar Bérénice Batutorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoToby Hodges avatar Toby Hodgesorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnne Fouilloux avatar Anne FouillouxAdelaide Rhodes avatar Adelaide Rhodesorcid logoLucille Delisle avatar Lucille Delisleorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoBert Droesbeke avatar Bert DroesbekeAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria Doyleorcid logoSaskia Hiltemann avatar Saskia HiltemannMarius van den Beek avatar Marius van den BeekMateusz Kuzak avatar Mateusz KuzakSimon Bray avatar Simon Brayorcid logoClea Siguret avatar Clea Siguretorcid logoNadia Goué avatar Nadia Gouéorcid logoArmin Dadras avatar Armin DadrasNiall Beard avatar Niall BeardYo Yehudi avatar Yo Yehudiorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosBoris Depoortere avatar Boris Depoortereorcid logoSimon Gladman avatar Simon Gladmanorcid logoWolfgang Maier avatar Wolfgang MaierMiguel Roncoroni avatar Miguel Roncoroni

Funding

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