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 logoMaria Doyle avatar Maria Doyleorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosDaniela Butano avatar Daniela ButanoElizabeth Sheets avatar Elizabeth Sheetsorcid logoSimon Gladman avatar Simon Gladmanorcid logoMartin Čech avatar Martin ČechTeresa Müller avatar Teresa MüllerMateusz Kuzak avatar Mateusz KuzakAnne Pajon avatar Anne Pajonorcid logoBjörn Grüning avatar Björn GrüningWilliam Durand avatar William DurandCharles Overbeck avatar Charles Overbeckorcid logoToby Hodges avatar Toby Hodgesorcid logoBérénice Batut avatar Bérénice BatutDeepti Varshney avatar Deepti VarshneyNic Herndon avatar Nic HerndonJon Trow avatar Jon Troworcid logoWendi Bacon avatar Wendi Baconorcid logoDave Clements avatar Dave Clementsorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoNicola Soranzo avatar Nicola SoranzoYo Yehudi avatar Yo YehudiEnis Afgan avatar Enis Afganorcid logoNate Coraor avatar Nate Coraororcid logoHelena Rasche avatar Helena Rascheorcid logoLucille Delisle avatar Lucille DelisleAnton Nekrutenko avatar Anton Nekrutenkoorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLaila Los avatar Laila LosAvani Khadilkar avatar Avani KhadilkarSimon Bray avatar Simon BrayMarius van den Beek avatar Marius van den Beekorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanBoris Depoortere avatar Boris Depoortereorcid logoAnthony Bretaudeau avatar Anthony BretaudeauNiall Beard avatar Niall BeardMiguel Roncoroni avatar Miguel Roncoroniorcid logoDelphine Lariviere avatar Delphine LariviereEkaterina Polkh avatar Ekaterina Polkhorcid logoBert Droesbeke avatar Bert DroesbekeAdelaide Rhodes avatar Adelaide Rhodesorcid logoJohn Chilton avatar John ChiltonAysam Guerler avatar Aysam Guerlerorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoSaskia Hiltemann avatar Saskia Hiltemann

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.