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 logoDelphine Lariviere avatar Delphine Lariviere

Contributors

This material was contributed to by:

orcid logoMartin Čech avatar Martin Čechorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoLucille Delisle avatar Lucille Delisleorcid logoHelena Rasche avatar Helena Rascheorcid logoArmin Dadras avatar Armin DadrasMateusz Kuzak avatar Mateusz Kuzakorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn GrüningAysam Guerler avatar Aysam GuerlerMarius van den Beek avatar Marius van den BeekMiguel Roncoroni avatar Miguel RoncoroniAnne Pajon avatar Anne PajonSimon Bray avatar Simon BrayEkaterina Polkh avatar Ekaterina PolkhAdelaide Rhodes avatar Adelaide Rhodesorcid logoSimon Gladman avatar Simon GladmanJon Trow avatar Jon TrowNic Herndon avatar Nic HerndonCharles Overbeck avatar Charles Overbeckorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoNicola Soranzo avatar Nicola SoranzoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMaria Doyle avatar Maria Doyleorcid logoTeresa Müller avatar Teresa Müllerorcid logoNate Coraor avatar Nate Coraororcid logoWendi Bacon avatar Wendi Baconorcid logoAnne Fouilloux avatar Anne FouillouxBoris Depoortere avatar Boris Depoortereorcid logoAnthony Bretaudeau avatar Anthony BretaudeauElizabeth Sheets avatar Elizabeth SheetsBartosz Walkowicz avatar Bartosz Walkowiczorcid logoToby Hodges avatar Toby Hodgesorcid logoJohn Chilton avatar John ChiltonYo Yehudi avatar Yo YehudiEnis Afgan avatar Enis Afganorcid logoDeepti Varshney avatar Deepti VarshneyAvani Khadilkar avatar Avani Khadilkarorcid logoAhmed Hamid Awan avatar Ahmed Hamid AwanDaniela Butano avatar Daniela ButanoNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoDave Clements avatar Dave ClementsWilliam Durand avatar William Durandorcid logoŁukasz Opioła avatar Łukasz Opiołaorcid logoLaila Los avatar Laila Los

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.