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 logoSaskia Hiltemann avatar Saskia HiltemannAvani Khadilkar avatar Avani KhadilkarNic Herndon avatar Nic Herndonorcid logoLucille Delisle avatar Lucille DelisleYo Yehudi avatar Yo YehudiJon Trow avatar Jon Troworcid logoWolfgang Maier avatar Wolfgang MaierAnne Pajon avatar Anne Pajonorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoŁukasz Opioła avatar Łukasz OpiołaEnis Afgan avatar Enis Afganorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoNate Coraor avatar Nate Coraororcid logoTeresa Müller avatar Teresa Müllerorcid logoMartin Čech avatar Martin ČechAnton Nekrutenko avatar Anton NekrutenkoAysam Guerler avatar Aysam GuerlerBartosz Walkowicz avatar Bartosz Walkowiczorcid logoYvan Le Bras avatar Yvan Le BrasAdelaide Rhodes avatar Adelaide Rhodesorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoArmin Dadras avatar Armin DadrasDaniela Butano avatar Daniela Butanoorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave Clementsorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoJohn Chilton avatar John ChiltonMateusz Kuzak avatar Mateusz Kuzakorcid logoLisanna Paladin avatar Lisanna Paladinorcid logoClea Siguret avatar Clea SiguretMiguel Roncoroni avatar Miguel Roncoroniorcid logoNadia Goué avatar Nadia GouéNiall Beard avatar Niall BeardBoris Depoortere avatar Boris DepoortereEkaterina Polkh avatar Ekaterina PolkhElizabeth Sheets avatar Elizabeth Sheetsorcid logoWendi Bacon avatar Wendi BaconSimon Bray avatar Simon BrayMarius van den Beek avatar Marius van den Beekorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoSimon Gladman avatar Simon Gladmanorcid logoToby Hodges avatar Toby Hodgesorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn Grüningorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosCharles Overbeck avatar Charles Overbeckorcid logoLaila Los avatar Laila Losorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMaria Doyle avatar Maria Doyleorcid logoDelphine Lariviere avatar Delphine Lariviere

Funding

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