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 logoSimon Gladman avatar Simon Gladmanorcid logoDave Clements avatar Dave Clementsorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMartin Čech avatar Martin Čechorcid logoMaria Doyle avatar Maria Doyleorcid logoJohn Chilton avatar John Chiltonorcid logoSaskia Hiltemann avatar Saskia HiltemannAysam Guerler avatar Aysam Guerlerorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoToby Hodges avatar Toby Hodgesorcid logoDaniela Schneider avatar Daniela SchneiderAvani Khadilkar avatar Avani Khadilkarorcid logoDeepti Varshney avatar Deepti VarshneyEkaterina Polkh avatar Ekaterina Polkhorcid logoLaila Los avatar Laila Losorcid logoTeresa Müller avatar Teresa MüllerAdelaide Rhodes avatar Adelaide Rhodesorcid logoWendi Bacon avatar Wendi BaconEnis Afgan avatar Enis Afganorcid logoArmin Dadras avatar Armin DadrasCharles Overbeck avatar Charles OverbeckMarius van den Beek avatar Marius van den BeekDaniela Butano avatar Daniela ButanoYo Yehudi avatar Yo YehudiAnne Pajon avatar Anne Pajonorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoDelphine Lariviere avatar Delphine LariviereBartosz Walkowicz avatar Bartosz Walkowiczorcid logoClea Siguret avatar Clea Siguretorcid logoBjörn Grüning avatar Björn Grüningorcid logoWolfgang Maier avatar Wolfgang MaierWilliam Durand avatar William DurandBoris Depoortere avatar Boris Depoortereorcid logoYvan Le Bras avatar Yvan Le BrasMateusz Kuzak avatar Mateusz KuzakMiguel Roncoroni avatar Miguel Roncoroniorcid logoNate Coraor avatar Nate CoraorSimon Bray avatar Simon BrayNic Herndon avatar Nic HerndonAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLucille Delisle avatar Lucille Delisleorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHelena Rasche avatar Helena RascheNiall Beard avatar Niall BeardElizabeth Sheets avatar Elizabeth Sheetsorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoŁukasz Opioła avatar Łukasz OpiołaJon Trow avatar Jon Troworcid logoNadia Goué avatar Nadia Goué

Funding

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