Using Galaxy and Managing your Data

A collection of microtutorials explaining various features of the Galaxy user interface and manipulating data within Galaxy.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Material

Uploading Data

These tutorials will help you get data into Galaxy, before you analyse it.

Lesson	Slides	Hands-on	Recordings
Getting data into Galaxy plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides	plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides
Rule Based Uploader collections tags tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Lecture & Tutorial (February 2021)		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Lecture & Tutorial (February 2021)
Rule Based Uploader: Advanced collections tags tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis ncbi covid19 plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Tutorial (February 2021) video Lecture (February 2021)	plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Tutorial (February 2021) video Lecture (February 2021)

Histories

Managing your analysis histories efficiently

Lesson	Slides	Hands-on	Recordings	Galaxy servers
Searching Your History tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Understanding Galaxy history system tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages

Making Data Manageable

Now that you have data in Galaxy, let's make it easier to work with through collections and structured data.

Lesson	Hands-on	Recordings
Group tags for complex experimental designs tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Multisample Analysis collections tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Name tags for following complex histories tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Using dataset collections collections tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Tutorial (August 2021)	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Tutorial (August 2021)

Workflows

Using Galaxy workflows to scale analysis

Lesson	Slides	Hands-on	Recordings	Galaxy servers
Automating Galaxy workflows using the command line workflows variant-analysis covid19 tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Lecture & Tutorial (February 2021) instances Galaxy Africa Galaxy India Galaxy Test Galaxy@GenOuest Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.org (Main) UseGalaxy.org.au		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Lecture & Tutorial (February 2021)	instances Galaxy Africa Galaxy India Galaxy Test Galaxy@GenOuest Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.org (Main) UseGalaxy.org.au
Creating, Editing and Importing Galaxy Workflows workflows tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas HyPhy HIV NGS Tools Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy PepSimili Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology covid19.UseGalaxy.fr		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas HyPhy HIV NGS Tools Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy PepSimili Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology covid19.UseGalaxy.fr
Extracting Workflows from Histories workflows tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Galaxy workflows in Dockstore plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides	plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides
Using Workflow Parameters workflows tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Tutorial (July 2022) instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas HyPhy HIV NGS Tools Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy PepSimili Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology covid19.UseGalaxy.fr		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Tutorial (July 2022)	instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas HyPhy HIV NGS Tools Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy PepSimili Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology covid19.UseGalaxy.fr
Workflow Reports workflows tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages video video Tutorial (July 2022) instances Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	video video Tutorial (July 2022)	instances Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@AuBi Galaxy@GenOuest GalaxyTrakr HiCExplorer Human Cell Atlas Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au

Analysing Data

Some advanced topics in data analysis.

Lesson	Hands-on	Galaxy servers
InterMine integration with Galaxy tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@GenOuest HiCExplorer Human Cell Atlas Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy Test Galaxy for Ecology Galaxy@GenOuest HiCExplorer Human Cell Atlas Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.no UseGalaxy.org (Main) UseGalaxy.org.au Virology
JupyterLab in Galaxy interactive-tools tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
RStudio in Galaxy interactive-tools tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages
Use Jupyter notebooks in Galaxy tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages

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	Galaxy servers
Downloading and Deleting Data in Galaxy tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages

Other

Assorted Tutorials

Lesson	Slides	Hands-on	Recordings	Galaxy servers
Submitting sequence data to ENA covid19 plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy for Ecology Galaxy@GenOuest HiCExplorer Human Cell Atlas Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.org.au Virology	plain text Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages Plain text slides	tutorial Toggle Dropdown Automatic translations Français 日本語 Español Português العربية More Languages		instances CLIP-Explorer ChemicalToolbox Climate Science Workbench Galaxy Africa Galaxy India Galaxy for Ecology Galaxy@GenOuest HiCExplorer Human Cell Atlas Machine Learning Workbench Metabolomics Metagenomics NanoGalaxy Plant Anaylsis Workbench Single Cell Omics workbench Street Science UseGalaxy.be UseGalaxy.eu UseGalaxy.fr UseGalaxy.org.au Virology

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.