Frequently Asked Questions

Tutorial Questions

I cannot run client tests because yarn is not installed.

Question: I cannot run client tests because yarn is not installed.

Make sure you have executed scripts/common_startup.sh and have activated the virtual environment (. .venv/vin/activate) in your current terminal session.

When I try to run a Selenium test, I get an error

Question: When I try to run a Selenium test, I get an error

If you get the following error:

selenium.common.exceptions.SessionNotCreatedException (...This version of ChromeDriver only supports Chrome version...)

Make sure that (a) the version of your ChromeDriver is the same as the version of Chrome:

$ chromedriver --version
$ chrome --version

If they are not the same:

  • download the appropriate version of ChromeDriver.
  • unzip the file
  • move the chromedriver file into the appropriate location.
    • On Linux, that could be /usr/bin, $HOME/.local/bin, etc.
    • Use the which command to check the location: $ which chromedriver
  • Make sure the permissions are correct (755).

General Questions

Can't find one of the tools for this tutorial?

To use the tools installed and available on the Galaxy server:

  1. At the top of the left tool panel, type in a tool name or datatype into the tool search box.
  2. Shorter keywords find more choices.
  3. Tools can also be directly browsed by category in the tool panel.

If you can’t find a tool you need for a tutorial on Galaxy, please:

  1. Check that you are using a compatible Galaxy server
    • Navigate to the overview box at the top of the tutorial
    • Find the “Supporting Materials” section
    • Check “Available on these Galaxies”
    • If your server is not listed here, the tutorial is not supported on your Galaxy server
    • You can create an account on one of the supporting Galaxies screenshot of overview box with available Galaxies section
  2. Use the Tutorial mode feature
    • Open your Galaxy server
    • Click on the icon on the top menu, this will open the GTN inside Galaxy.
    • Navigate to your tutorial
    • Tool names in tutorials will be blue buttons that open the correct tool for you
    • Note: this does not work for all tutorials (yet) gif showing how GTN-in-Galaxy works
  3. Still not finding the tool?

Running into an error?

When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.

  1. Expand the red history dataset by clicking on it.
    • Sometimes you can already see an error message here

  2. View the error message by clicking on the bug icon

  3. Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
    • Expand the history item
    • Click on the icon
    • Scroll down to the Job Information section to view the 2 logs:
      • Tool Standard Output
      • Tool Standard Error
    • For more information about specific tool errors, please see the Troubleshooting section
  4. Submit a bug report! If you are still unsure what the problem is.
    • Click on the bug icon
    • Write down any information you think might help solve the problem
      • See this FAQ on how to write good bug reports
    • Click Report button
  5. Ask for help!


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