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
    • 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
    Multisample Analysis
    Name tags for following complex histories
    Using dataset collections

    • Workflows

    Using Galaxy workflows to scale analysis

    Lesson Slides Hands-on Recordings
    Automating Galaxy workflows using the command line
    • 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

    Other


    Assorted other tutorials

    Lesson Slides Hands-on Recordings
    Submitting raw sequencing reads 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.

    Maintainers

    This material is maintained by:

    orcid logoAvatarJennifer Hillman-Jackson orcid 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:

    AvatarSimon Bray AvatarWolfgang Maier AvatarMarius van den Beek AvatarSimon Gladman orcid logoAvatarHelena Rasche AvatarDave Clements AvatarAvani Khadilkar AvatarElizabeth Sheets AvatarCharles Overbeck AvatarEnis Afgan AvatarAnne Pajon AvatarMaria Doyle orcid logoAvatarSaskia Hiltemann AvatarDaniela Butano AvatarYo Yehudi AvatarAnne Fouilloux AvatarAnton Nekrutenko orcid logoAvatarBérénice Batut orcid logoAvatarFotis E. Psomopoulos orcid logoAvatarToby Hodges AvatarErasmus+ Programme orcid logoAvatarJohn Chilton AvatarJon Trow AvatarAdelaide Rhodes AvatarMiguel Roncoroni AvatarMartin Čech AvatarDelphine Lariviere