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Submit a Pull Request to Galaxy ​

With your visualization published to npm, the next step is to submit a pull request to the Galaxy development repository. This pull request should include your XML wrapper file and, optionally, a logo file in svg format.

Note: Replace MY_VISUALIZATION with your visualization name in the following instructions.

Step 1: Fork and Clone the Galaxy Repository ​

Fork the Galaxy repository available at Galaxy Project on GitHub and clone it to your local machine.

Step 2: Create a Branch for Your Visualization ​

Create a new branch specifically for your visualization:

bash
git branch MY_VISUALIZATION
git checkout MY_VISUALIZATION

Step 3: Set Up Your Visualization Directory ​

  1. Create a directory for your visualization in the Galaxy repository at config/plugins/visualizations/MY_VISUALIZATION.

  2. Copy the XML file (MY_VISUALIZATION.xml) generated during development into a subdirectory named config:

plaintext
config/plugins/visualizations/MY_VISUALIZATION/config/MY_VISUALIZATION.xml

Step 4: Verify XML Requirements and Data Sources ​

  1. Ensure the requirements section in your XML file specifies the correct npm package name and version.
  2. Confirm the data_sources section in the XML lists the appropriate datatype extension(s) compatible with your visualization.

Optionally, include a logo file (logo.svg) for your visualization by placing it in a static subdirectory:

plaintext
config/plugins/visualizations/MY_VISUALIZATION/static/logo.svg

Step 6: Update the Gulpfile ​

In the Galaxy root directory, open client/gulpfile.js and add the name of your visualization to the INSTALL_PLUGIN_BUILD_IDS list.

Step 7: Run Galaxy and Test Your Visualization ​

  1. Start Galaxy by running the following command:

    bash
    ./run.sh

  2. Upload a test file to your Galaxy history, ensuring it has the correct data type for your visualization.

  3. Open your visualization from the Activity Bar to view and test your uploaded dataset.

🎉 Thank you for your contribution! ​

Following these steps will prepare your visualization for integration with Galaxy. Once everything is set up, you can submit your pull request.