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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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

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

Contributors

This material was contributed to by:

orcid logoArmin Dadras avatar Armin Dadrasorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLucille Delisle avatar Lucille Delisleorcid logoYvan Le Bras avatar Yvan Le BrasNiall Beard avatar Niall Beardorcid logoBjörn Grüning avatar Björn Grüningorcid logoNicola Soranzo avatar Nicola SoranzoTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine LariviereJon Trow avatar Jon Troworcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoBérénice Batut avatar Bérénice Batutorcid logoMartin Čech avatar Martin ČechAdelaide Rhodes avatar Adelaide Rhodesorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoToby Hodges avatar Toby HodgesEkaterina Polkh avatar Ekaterina Polkhorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnne Fouilloux avatar Anne FouillouxNic Herndon avatar Nic HerndonYo Yehudi avatar Yo YehudiAysam Guerler avatar Aysam Guerlerorcid logoJohn Chilton avatar John ChiltonSimon Bray avatar Simon Brayorcid logoSaskia Hiltemann avatar Saskia HiltemannMateusz Kuzak avatar Mateusz KuzakMiguel Roncoroni avatar Miguel RoncoroniAnne Pajon avatar Anne PajonCharles Overbeck avatar Charles OverbeckMarius van den Beek avatar Marius van den Beekorcid logoWolfgang Maier avatar Wolfgang MaierBoris Depoortere avatar Boris Depoortereorcid logoDave Clements avatar Dave ClementsAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena RascheWilliam Durand avatar William DurandDeepti Varshney avatar Deepti VarshneyAvani Khadilkar avatar Avani Khadilkarorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaila Los avatar Laila LosDaniela Butano avatar Daniela Butanoorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoMaria Doyle avatar Maria Doyleorcid logoNate Coraor avatar Nate Coraororcid logoWendi Bacon avatar Wendi BaconElizabeth Sheets avatar Elizabeth SheetsEnis Afgan avatar Enis Afgan

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.