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 (slides) and tutorial (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
Importing (uploading) data from Onedata
Onedata user-owned storage
Rule Based Uploader
Rule Based Uploader: Advanced
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis

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

Workflows

Using Galaxy workflows to scale analysis

Lesson Slides Hands-on Recordings
Annotate, prepare tests and publish Galaxy workflows in workflow registries
Automating Galaxy workflows using the command line
Creating high resolution images of Galaxy Workflows
Creating, Editing and Importing Galaxy Workflows
Extracting Workflows from Histories
Galaxy workflows in Dockstore
Using Workflow Parameters
Workflow Reports

Analysing Data

Some advanced topics in data analysis.

Lesson Slides Hands-on Recordings
InterMine integration with Galaxy
JupyterLab in Galaxy
RStudio in Galaxy
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
Exporting to Onedata remote

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Getting started with Onedata distributed storage
Submitting sequence data to ENA

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 logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa Müller

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoHelena Rasche avatar Helena Rascheorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoSimon Gladman avatar Simon Gladmanorcid logoTeresa Müller avatar Teresa MüllerMiguel Roncoroni avatar Miguel RoncoroniAysam Guerler avatar Aysam Guerlerorcid logoToby Hodges avatar Toby Hodgesorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoNadia Goué avatar Nadia Gouéorcid logoBérénice Batut avatar Bérénice Batutorcid logoMartin Čech avatar Martin ČechYo Yehudi avatar Yo Yehudiorcid logoDelphine Lariviere avatar Delphine LariviereCharles Overbeck avatar Charles OverbeckEkaterina Polkh avatar Ekaterina PolkhWilliam Durand avatar William DurandAnton Nekrutenko avatar Anton NekrutenkoMateusz Kuzak avatar Mateusz Kuzakorcid logoDave Clements avatar Dave ClementsEnis Afgan avatar Enis AfganAdelaide Rhodes avatar Adelaide Rhodesorcid logoLucille Delisle avatar Lucille Delisleorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoLaila Los avatar Laila LosBartosz Walkowicz avatar Bartosz WalkowiczMarius van den Beek avatar Marius van den Beekorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoDaniela Schneider avatar Daniela SchneiderAvani Khadilkar avatar Avani KhadilkarSimon Bray avatar Simon BrayBoris Depoortere avatar Boris Depoortereorcid logoClea Siguret avatar Clea Siguretorcid logoBjörn Grüning avatar Björn GrüningJon Trow avatar Jon TrowAnne Pajon avatar Anne Pajonorcid logoJohn Chilton avatar John Chiltonorcid logoMaria Doyle avatar Maria Doyleorcid logoNate Coraor avatar Nate Coraororcid logoArmin Dadras avatar Armin Dadrasorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoWendi Bacon avatar Wendi Baconorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoCristóbal Gallardo avatar Cristóbal GallardoNiall Beard avatar Niall BeardDaniela Butano avatar Daniela ButanoNic Herndon avatar Nic HerndonElizabeth Sheets avatar Elizabeth Sheetsorcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

These individuals or organisations provided funding support for the development of this resource