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

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Contributors

This material was contributed to by:

Bartosz Walkowicz avatar Bartosz WalkowiczYo Yehudi avatar Yo YehudiAvani Khadilkar avatar Avani Khadilkarorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNate Coraor avatar Nate CoraorAnton Nekrutenko avatar Anton NekrutenkoAysam Guerler avatar Aysam Guerlerorcid logoLisanna Paladin avatar Lisanna PaladinJon Trow avatar Jon Troworcid logoŁukasz Opioła avatar Łukasz OpiołaDaniela Butano avatar Daniela Butanoorcid logoBert Droesbeke avatar Bert DroesbekeAdelaide Rhodes avatar Adelaide RhodesSimon Bray avatar Simon BrayEnis Afgan avatar Enis AfganNic Herndon avatar Nic Herndonorcid logoToby Hodges avatar Toby Hodgesorcid logoDave Clements avatar Dave Clementsorcid logoMartin Čech avatar Martin Čechorcid logoAnne Fouilloux avatar Anne FouillouxNiall Beard avatar Niall BeardAnne Pajon avatar Anne PajonElizabeth Sheets avatar Elizabeth Sheetsorcid logoWolfgang Maier avatar Wolfgang MaierMarius van den Beek avatar Marius van den Beekorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBérénice Batut avatar Bérénice Batutorcid logoNicola Soranzo avatar Nicola SoranzoCharles Overbeck avatar Charles Overbeckorcid logoBjörn Grüning avatar Björn Grüningorcid logoClea Siguret avatar Clea Siguretorcid logoMaria Doyle avatar Maria DoyleEkaterina Polkh avatar Ekaterina PolkhBoris Depoortere avatar Boris Depoortereorcid logoNadia Goué avatar Nadia GouéMateusz Kuzak avatar Mateusz Kuzakorcid logoArmin Dadras avatar Armin Dadrasorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoJohn Chilton avatar John Chiltonorcid logoSimon Gladman avatar Simon Gladmanorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoLucille Delisle avatar Lucille Delisleorcid logoLaila Los avatar Laila Losorcid logoTeresa Müller avatar Teresa MüllerWilliam Durand avatar William DurandMiguel Roncoroni avatar Miguel Roncoroniorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoWendi Bacon avatar Wendi Baconorcid logoHelena Rasche avatar Helena Rasche

Funding

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