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 () and 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
storage
Onedata user-owned storage
storage
Rule Based Uploader
collections tags
Rule Based Uploader: Advanced
collections tags
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
ncbi covid19

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
collections

Workflows

Using Galaxy workflows to scale analysis

Lesson Slides Hands-on Recordings
Automating Galaxy workflows using the command line
workflows variant-analysis covid19
Creating high resolution images of Galaxy Workflows
workflows
Creating, Editing and Importing Galaxy Workflows
workflows
Extracting Workflows from Histories
workflows
Galaxy workflows in Dockstore
Using Workflow Parameters
workflows
Workflow Reports
workflows

Analysing Data

Some advanced topics in data analysis.

Lesson Slides Hands-on Recordings
InterMine integration with Galaxy
gmod intermine
JupyterLab in Galaxy
interactive-tools
RStudio in Galaxy
interactive-tools
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
storage

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
Getting started with Onedata distributed storage
storage
Submitting sequence data to ENA
covid19

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 logoHelena Rasche avatar Helena Rasche

Contributors

This material was contributed to by:

Anne Pajon avatar Anne PajonBartosz Walkowicz avatar Bartosz WalkowiczWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola SoranzoEkaterina Polkh avatar Ekaterina Polkhorcid logoDave Clements avatar Dave Clementsorcid logoWendi Bacon avatar Wendi BaconMateusz Kuzak avatar Mateusz Kuzakorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoJohn Chilton avatar John Chiltonorcid logoSimon Gladman avatar Simon Gladmanorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosAnton Nekrutenko avatar Anton Nekrutenkoorcid logoLucille Delisle avatar Lucille DelisleJon Trow avatar Jon TrowTeresa Müller avatar Teresa MüllerNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLaila Los avatar Laila Losorcid logoNate Coraor avatar Nate CoraorMiguel Roncoroni avatar Miguel RoncoroniNic Herndon avatar Nic HerndonEnis Afgan avatar Enis Afganorcid logoBjörn Grüning avatar Björn Grüningorcid logoHelena Rasche avatar Helena RascheElizabeth Sheets avatar Elizabeth Sheetsorcid logoMaria Doyle avatar Maria DoyleCharles Overbeck avatar Charles OverbeckDaniela Butano avatar Daniela ButanoDeepti Varshney avatar Deepti Varshneyorcid logoŁukasz Opioła avatar Łukasz OpiołaSimon Bray avatar Simon Brayorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoBérénice Batut avatar Bérénice BatutYo Yehudi avatar Yo YehudiAvani Khadilkar avatar Avani Khadilkarorcid logoToby Hodges avatar Toby Hodgesorcid logoSaskia Hiltemann avatar Saskia HiltemannAdelaide Rhodes avatar Adelaide Rhodesorcid logoMartin Čech avatar Martin ČechBoris Depoortere avatar Boris DepoortereMarius van den Beek avatar Marius van den BeekAysam Guerler avatar Aysam Guerlerorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoArmin Dadras avatar Armin Dadras

Funding

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

Logo
Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.