Create A Galaxy Workflow

Convert your analysis history into a workflow

Galaxy records every tool you run and the parameters used. You can convert this history into a workflow to reuse later.

TipExtract workflow

  1. Clean up your history: remove any failed (red) jobs

  2. Click (History options) → Extract workflow

    extract-workflow

  3. Select the steps to include

  4. Replace the workflow name (e.g., FASTQ Emoji Workflow)

  5. Rename the workflow input (e.g., FASTQ reads)

    workflow-rename

  6. Click Create Workflow

TipKey Points
  • The Galaxy interface has an activity bar on the left, a tool (or other activated) panel next to it (if expanded), viewing pane in the middle, and a history of your data analysis on the right.
  • You can create a new history for each analysis. All your histories are saved.
  • To get data into Galaxy, you can upload a file by pasting in a web address. There are other ways to get data into Galaxy (not covered in this tutorial): you can upload a file from your computer, and you can import an entire history.
  • Choose a tool and change any settings for your analysis.
  • Run the tool. The output files will be saved at the top of your history.
  • View the output files by clicking the eye icon.
  • View all your histories and move files between them. Switch to a different history.
  • Log out of your Galaxy server. When you log back in (to the same server), your histories will all be there.