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.


Uploading Data

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

Lesson Slides Hands-on Recordings
Getting data into Galaxy
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Rule Based Uploader tutorial
  • Rule Based Uploader: Advanced tutorial
    SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis plain text tutorial
  • 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 tutorial
    Name tags for following complex histories
    Using dataset collections tutorial
  • Workflows

    Using Galaxy workflows to scale analysis

    Lesson Slides Hands-on Recordings
    Automating Galaxy workflows using the command line tutorial
  • Creating, Editing and Importing Galaxy Workflows tutorial
    Extracting Workflows from Histories tutorial
    Galaxy workflows in Dockstore
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    Using Workflow Parameters tutorial
    Workflow Reports tutorial

    Analysing Data

    Some advanced topics in data analysis.

    Lesson Slides Hands-on Recordings
    InterMine integration with Galaxy
    JupyterLab in Galaxy tutorial
    RStudio in Galaxy tutorial
    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


    Assorted other tutorials

    Lesson Slides Hands-on Recordings
    Submitting raw sequencing reads to ENA plain text tutorial

    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.


    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.


    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 AvatarJohn Chilton AvatarJon Trow AvatarAdelaide Rhodes AvatarMiguel Roncoroni AvatarMartin Čech AvatarDelphine Lariviere