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.

Follow topic updates with our RSS Feed

Community Resources

Community Home Maintainer Home

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 logoWendi Bacon avatar Wendi Baconorcid logoLucille Delisle avatar Lucille DelisleNiall Beard avatar Niall BeardAysam Guerler avatar Aysam Guerlerorcid logoSaskia Hiltemann avatar Saskia HiltemannAvani Khadilkar avatar Avani KhadilkarMarius van den Beek avatar Marius van den Beekorcid logoSimon Gladman avatar Simon Gladmanorcid logoBert Droesbeke avatar Bert DroesbekeAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoToby Hodges avatar Toby Hodgesorcid logoWolfgang Maier avatar Wolfgang MaierSimon Bray avatar Simon BrayAnne Pajon avatar Anne PajonWilliam Durand avatar William Durandorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoAnthony Bretaudeau avatar Anthony BretaudeauElizabeth Sheets avatar Elizabeth SheetsTeresa Müller avatar Teresa MüllerDaniela Butano avatar Daniela Butanoorcid logoCristóbal Gallardo avatar Cristóbal GallardoCharles Overbeck avatar Charles OverbeckAdelaide Rhodes avatar Adelaide Rhodesorcid logoJohn Chilton avatar John Chiltonorcid logoNate Coraor avatar Nate Coraororcid logoLaila Los avatar Laila LosEnis Afgan avatar Enis Afganorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMaria Doyle avatar Maria Doyleorcid logoDelphine Lariviere avatar Delphine LariviereMiguel Roncoroni avatar Miguel Roncoroniorcid logoArmin Dadras avatar Armin DadrasNic Herndon avatar Nic HerndonDeepti Varshney avatar Deepti Varshneyorcid logoNicola Soranzo avatar Nicola SoranzoMateusz Kuzak avatar Mateusz KuzakJon Trow avatar Jon TrowBoris Depoortere avatar Boris DepoortereEkaterina Polkh avatar Ekaterina Polkhorcid logoBérénice Batut avatar Bérénice Batutorcid logoDave Clements avatar Dave Clementsorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoHelena Rasche avatar Helena Rascheorcid logoMartin Čech avatar Martin ČechYo Yehudi avatar Yo Yehudi

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.