DEVELOPMENT.md

Development and Release Documentation

Releasing to ToolShed

How to submit a tool to the Galaxy ToolShed:

1. Create an account on the ToolShed
2. Create a $HOME/.planemo.yml file with the following content:

shed_username: $USER # your ToolShed username
sheds:
  toolshed:
    key: $KEY        # your ToolShed API key, under 'User > API Keys'
    email: $EMAIL    # your ToolShed email
    password: $PASS  # your ToolShed password

3. Install Planemo:

pip install planemo

4. Validate your tool XML:

planemo lint monophylizer.xml

5. Test your tool:

planemo test monophylizer.xml

6. Publish your tool:

planemo shed_create --shed_target toolshed

7. Update your tool:

planemo shed_update --shed_target toolshed

CI/CD and Testing

This repository includes GitHub Actions workflows for continuous testing and publishing:

Automated Publishing to Galaxy Toolshed

The planemo-publish.yml workflow automatically publishes the tool to the Galaxy Toolshed when a new version is tagged. To use this workflow:

1. Set up the following repository secrets (Settings > Secrets and variables > Actions):

   • USER: Your Galaxy Toolshed username
   • KEY: Your Toolshed API key (found under User > API Keys)
   • EMAIL: Your Toolshed account email
   • PASS: Your Toolshed account password

2. Create a new tag to trigger publishing:

   git tag v1.0.0
   git push origin v1.0.0

The workflow will automatically:

• Install Planemo and dependencies
• Create the Planemo configuration file
• Update the existing tool in the toolshed (or create it if it doesn't exist yet)

Viewing Test Outputs

The planemo-test.yml workflow automatically runs tests on every push and pull request. It captures all temporary output files generated during testing and uploads them as artifacts. You can:

1. Go to the Actions tab in GitHub
2. Click on a workflow run
3. Scroll down to "Artifacts" section
4. Download planemo-test-outputs to view the actual output files generated during testing
5. The workflow logs also display the contents of TSV output files inline

This is useful for:

• Debugging test failures
• Verifying the actual output format
• Updating test-data files when the tool behavior changes