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 logoNate Coraor avatar Nate Coraororcid logoYvan Le Bras avatar Yvan Le Brasorcid logoNadia Goué avatar Nadia Gouéorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoWendi Bacon avatar Wendi BaconBartosz Walkowicz avatar Bartosz Walkowiczorcid logoJohn Chilton avatar John ChiltonMateusz Kuzak avatar Mateusz Kuzakorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoArmin Dadras avatar Armin Dadrasorcid logoBjörn Grüning avatar Björn Grüningorcid logoMartin Čech avatar Martin Čechorcid logoBert Droesbeke avatar Bert DroesbekeNic Herndon avatar Nic Herndonorcid logoHelena Rasche avatar Helena RascheAnne Pajon avatar Anne Pajonorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoTeresa Müller avatar Teresa MüllerNiall Beard avatar Niall Beardorcid logoNicola Soranzo avatar Nicola SoranzoMiguel Roncoroni avatar Miguel Roncoroniorcid logoLaila Los avatar Laila LosMarius van den Beek avatar Marius van den Beekorcid logoMaria Doyle avatar Maria Doyleorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDave Clements avatar Dave ClementsAdelaide Rhodes avatar Adelaide Rhodesorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoClea Siguret avatar Clea SiguretYo Yehudi avatar Yo Yehudiorcid logoToby Hodges avatar Toby Hodgesorcid logoDeepti Varshney avatar Deepti VarshneyCharles Overbeck avatar Charles OverbeckAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLisanna Paladin avatar Lisanna PaladinJon Trow avatar Jon Troworcid logoDaniela Schneider avatar Daniela Schneiderorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoSimon Gladman avatar Simon GladmanEkaterina Polkh avatar Ekaterina PolkhAvani Khadilkar avatar Avani KhadilkarDaniela Butano avatar Daniela ButanoAysam Guerler avatar Aysam Guerlerorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoWilliam Durand avatar William DurandElizabeth Sheets avatar Elizabeth Sheetsorcid logoLucille Delisle avatar Lucille DelisleBoris Depoortere avatar Boris DepoortereSimon Bray avatar Simon BrayEnis Afgan avatar Enis Afgan

Funding

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