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:

Jon Trow avatar Jon TrowAdelaide Rhodes avatar Adelaide Rhodesorcid logoMartin Čech avatar Martin Čechorcid logoMaria Doyle avatar Maria DoyleWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal GallardoMiguel Roncoroni avatar Miguel Roncoroniorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoLaila Los avatar Laila Losorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoBert Droesbeke avatar Bert DroesbekeEnis Afgan avatar Enis AfganMateusz Kuzak avatar Mateusz Kuzakorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosDaniela Butano avatar Daniela ButanoBoris Depoortere avatar Boris Depoortereorcid logoSaskia Hiltemann avatar Saskia HiltemannAnne Pajon avatar Anne Pajonorcid logoNate Coraor avatar Nate CoraorAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena RascheAvani Khadilkar avatar Avani Khadilkarorcid logoBérénice Batut avatar Bérénice BatutNic Herndon avatar Nic HerndonDeepti Varshney avatar Deepti Varshneyorcid logoWendi Bacon avatar Wendi BaconElizabeth Sheets avatar Elizabeth SheetsNiall Beard avatar Niall BeardAysam Guerler avatar Aysam Guerlerorcid logoBjörn Grüning avatar Björn Grüningorcid logoSimon Gladman avatar Simon Gladmanorcid logoArmin Dadras avatar Armin DadrasYo Yehudi avatar Yo YehudiTeresa Müller avatar Teresa Müllerorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanMarius van den Beek avatar Marius van den Beekorcid logoDave Clements avatar Dave Clementsorcid logoJohn Chilton avatar John Chiltonorcid logoAnne Fouilloux avatar Anne FouillouxCharles Overbeck avatar Charles OverbeckSimon Bray avatar Simon Brayorcid logoLucille Delisle avatar Lucille Delisleorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoToby Hodges avatar Toby HodgesEkaterina Polkh avatar Ekaterina Polkh

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.