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 () and 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
Rule Based Uploader
collections tags
Rule Based Uploader: Advanced
collections tags
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
ncbi covid19

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
collections

Workflows

Using Galaxy workflows to scale analysis

Lesson Slides Hands-on Recordings
Automating Galaxy workflows using the command line
workflows variant-analysis covid19
Creating high resolution images of Galaxy Workflows
workflows
Creating, Editing and Importing Galaxy Workflows
workflows
Extracting Workflows from Histories
workflows
Galaxy workflows in Dockstore
Using Workflow Parameters
workflows
Workflow Reports
workflows

Analysing Data

Some advanced topics in data analysis.

Lesson Slides Hands-on Recordings
InterMine integration with Galaxy
gmod intermine
JupyterLab in Galaxy
interactive-tools
RStudio in Galaxy
interactive-tools
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

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Submitting sequence data to ENA
covid19

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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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jackson orcid logoHelena Rasche avatar Helena Rasche

Contributors

This material was contributed to by:

orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau orcid logoBert Droesbeke avatar Bert Droesbeke orcid logoAnne Fouilloux avatar Anne Fouilloux Avani Khadilkar avatar Avani Khadilkar Mateusz Kuzak avatar Mateusz Kuzak orcid logoAhmed Hamid Awan avatar Ahmed Hamid Awan Ekaterina Polkh avatar Ekaterina Polkh orcid logoLucille Delisle avatar Lucille Delisle orcid logoHelena Rasche avatar Helena Rasche Yo Yehudi avatar Yo Yehudi Adelaide Rhodes avatar Adelaide Rhodes Charles Overbeck avatar Charles Overbeck Daniela Butano avatar Daniela Butano orcid logoMartin Čech avatar Martin Čech Deepti Varshney avatar Deepti Varshney orcid logoMaria Doyle avatar Maria Doyle orcid logoYvan Le Bras avatar Yvan Le Bras orcid logoBjörn Grüning avatar Björn Grüning Niall Beard avatar Niall Beard orcid logoJohn Chilton avatar John Chilton Boris Depoortere avatar Boris Depoortere Oleg Zharkov avatar Oleg Zharkov Anne Pajon avatar Anne Pajon Matthias Bernt avatar Matthias Bernt Simon Bray avatar Simon Bray William Durand avatar William Durand orcid logoNicola Soranzo avatar Nicola Soranzo Anton Nekrutenko avatar Anton Nekrutenko Aysam Guerler avatar Aysam Guerler orcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano Elizabeth Sheets avatar Elizabeth Sheets orcid logoBérénice Batut avatar Bérénice Batut orcid logoDelphine Lariviere avatar Delphine Lariviere Marius van den Beek avatar Marius van den Beek orcid logoCristóbal Gallardo avatar Cristóbal Gallardo Enis Afgan avatar Enis Afgan Mehmet Tekman avatar Mehmet Tekman Nic Herndon avatar Nic Herndon orcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulos orcid logoToby Hodges avatar Toby Hodges Jon Trow avatar Jon Trow orcid logoSimon Gladman avatar Simon Gladman Teresa Müller avatar Teresa Müller David López avatar David López orcid logoLaila Los avatar Laila Los orcid logoWolfgang Maier avatar Wolfgang Maier Miguel Roncoroni avatar Miguel Roncoroni orcid logoSaskia Hiltemann avatar Saskia Hiltemann Gildas Le Corguillé avatar Gildas Le Corguillé orcid logoDave Clements avatar Dave Clements orcid logoWendi Bacon avatar Wendi Bacon orcid logoNate Coraor avatar Nate Coraor

Funding

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

Logo
Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.