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.

Follow topic updates rss-feed 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 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:

Nic Herndon avatar Nic HerndonSimon Bray avatar Simon BrayMiguel Roncoroni avatar Miguel RoncoroniEnis Afgan avatar Enis Afganorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoDave Clements avatar Dave ClementsAysam Guerler avatar Aysam GuerlerBoris Depoortere avatar Boris DepoortereAnne Pajon avatar Anne Pajonorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLucille Delisle avatar Lucille DelisleYo Yehudi avatar Yo Yehudiorcid logoDeepti Varshney avatar Deepti VarshneyMarius van den Beek avatar Marius van den BeekAvani Khadilkar avatar Avani Khadilkarorcid logoWendi Bacon avatar Wendi Baconorcid logoNadia Goué avatar Nadia Gouéorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoArmin Dadras avatar Armin DadrasNiall Beard avatar Niall Beardorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBjörn Grüning avatar Björn Grüningorcid logoDaniela Schneider avatar Daniela SchneiderElizabeth Sheets avatar Elizabeth Sheetsorcid logoBérénice Batut avatar Bérénice BatutDaniela Butano avatar Daniela ButanoEkaterina Polkh avatar Ekaterina Polkhorcid logoNicola Soranzo avatar Nicola SoranzoMateusz Kuzak avatar Mateusz KuzakBartosz Walkowicz avatar Bartosz Walkowiczorcid logoWolfgang Maier avatar Wolfgang MaierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria Doyleorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoTeresa Müller avatar Teresa Müllerorcid logoMartin Čech avatar Martin Čechorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoSimon Gladman avatar Simon GladmanWilliam Durand avatar William Durandorcid logoClea Siguret avatar Clea Siguretorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoToby Hodges avatar Toby HodgesAdelaide Rhodes avatar Adelaide Rhodesorcid logoLaila Los avatar Laila Losorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoJohn Chilton avatar John Chiltonorcid logoHelena Rasche avatar Helena RascheCharles Overbeck avatar Charles OverbeckJon Trow avatar Jon Troworcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNate Coraor avatar Nate Coraor

Funding

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