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 () and 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
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
Multisample Analysis
collections
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, 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
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

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings
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.

Maintainers

This material is maintained by:

orcid logoAvatarJennifer Hillman-Jacksonorcid logoAvatarHelena Rasche

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

orcid logoAvatarBérénice BatutAvatarCharles Overbeckorcid logoAvatarSimon Gladmanorcid logoAvatarCristóbal Gallardoorcid logoAvatarMaria DoyleAvatarAnne Pajonorcid logoAvatarDave Clementsorcid logoAvatarBert DroesbekeAvatarAdelaide RhodesAvatarJon Troworcid logoAvatarHelena RascheAvatarAnton Nekrutenkoorcid logoAvatarBjörn GrüningAvatarYo Yehudiorcid logoAvatarFotis E. Psomopoulosorcid logoAvatarAnne FouillouxAvatarElizabeth SheetsAvatarErasmus+ ProgrammeAvatarSimon BrayAvatarAysam Guerlerorcid logoAvatarMartin Čechorcid logoAvatarSaskia HiltemannAvatarEkaterina PolkhAvatarAvani Khadilkarorcid logoAvatarDelphine LariviereAvatarEnis Afganorcid logoAvatarJohn ChiltonAvatarMiguel RoncoroniAvatarMarius van den BeekAvatarDaniela Butanoorcid logoAvatarWolfgang Maierorcid logoAvatarToby Hodges