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
Introduction to the Dataverse Integration in Galaxy
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
Accessing IIIF from within Galaxy
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 logoBert Droesbeke avatar Bert DroesbekeMateusz Kuzak avatar Mateusz Kuzakorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoTeresa Müller avatar Teresa MüllerJon Trow avatar Jon Troworcid logoBérénice Batut avatar Bérénice BatutAysam Guerler avatar Aysam Guerlerorcid logoHelena Rasche avatar Helena Rascheorcid logoDelphine Lariviere avatar Delphine LariviereEkaterina Polkh avatar Ekaterina PolkhYo Yehudi avatar Yo Yehudiorcid logoMarius van den Beek avatar Marius van den BeekAvani Khadilkar avatar Avani Khadilkarorcid logoPavankumar Videm avatar Pavankumar VidemAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNadia Goué avatar Nadia Gouéorcid logoAnup Kumar avatar Anup Kumarorcid logoWolfgang Maier avatar Wolfgang MaierBartosz Walkowicz avatar Bartosz WalkowiczSimon Bray avatar Simon Brayorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoWendi Bacon avatar Wendi BaconCharles Overbeck avatar Charles Overbeckorcid logoMaria Doyle avatar Maria DoyleNic Herndon avatar Nic Herndonorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoDave Clements avatar Dave Clementsorcid logoNate Coraor avatar Nate CoraorAdelaide Rhodes avatar Adelaide Rhodesorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoMartin Čech avatar Martin ČechWilliam Durand avatar William Durandorcid logoAnne Fouilloux avatar Anne FouillouxGildas Le Corguillé avatar Gildas Le Corguilléorcid logoArmin Dadras avatar Armin DadrasEnis Afgan avatar Enis Afganorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoLucille Delisle avatar Lucille DelisleDaniela Butano avatar Daniela Butanoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn GrüningBoris Depoortere avatar Boris Depoortereorcid logoJohn Chilton avatar John ChiltonElizabeth Sheets avatar Elizabeth Sheetsorcid logoToby Hodges avatar Toby Hodgesorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnne Pajon avatar Anne Pajonorcid logoSimon Gladman avatar Simon Gladmanorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoClea Siguret avatar Clea SiguretRita Gautschy avatar Rita Gautschyorcid logoDeepti Varshney avatar Deepti VarshneyNiall Beard avatar Niall Beardorcid logoLaila Los avatar Laila LosMiguel Roncoroni avatar Miguel Roncoroni

Funding

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