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 logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton NekrutenkoBoris Depoortere avatar Boris Depoortereorcid logoAnne Fouilloux avatar Anne FouillouxJon Trow avatar Jon Troworcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMartin Čech avatar Martin Čechorcid logoBérénice Batut avatar Bérénice BatutAysam Guerler avatar Aysam Guerlerorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoDave Clements avatar Dave Clementsorcid logoMaria Doyle avatar Maria Doyleorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoWendi Bacon avatar Wendi Baconorcid logoToby Hodges avatar Toby HodgesDaniela Butano avatar Daniela Butanoorcid logoNate Coraor avatar Nate CoraorNic Herndon avatar Nic HerndonCharles Overbeck avatar Charles OverbeckMateusz Kuzak avatar Mateusz KuzakDeepti Varshney avatar Deepti Varshneyorcid logoBjörn Grüning avatar Björn Grüningorcid logoHelena Rasche avatar Helena Rascheorcid logoJohn Chilton avatar John ChiltonMiguel Roncoroni avatar Miguel RoncoroniNiall Beard avatar Niall BeardSimon Bray avatar Simon BrayAdelaide Rhodes avatar Adelaide Rhodesorcid logoBert Droesbeke avatar Bert DroesbekeElizabeth Sheets avatar Elizabeth Sheetsorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaila Los avatar Laila Losorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSimon Gladman avatar Simon GladmanYo Yehudi avatar Yo YehudiWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola SoranzoEnis Afgan avatar Enis AfganTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine LariviereMarius van den Beek avatar Marius van den Beekorcid logoLucille Delisle avatar Lucille DelisleEkaterina Polkh avatar Ekaterina PolkhAnne Pajon avatar Anne PajonAvani Khadilkar avatar Avani Khadilkar

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.