Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at

If you are reporting a bug, please include:

  • Your operating system name and version, versions of other relevant software such as Galaxy or Docker.

  • Links to relevant tools.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” is open to whoever wants to implement it.

Write Documentation

Planemo could always use more documentation, whether as part of the official Planemo docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at

If you are proposing a feature:

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • This will hopefully become a community-driven project and contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up planemo for local development.

  1. Fork the planemo repo on GitHub.

  2. Clone your fork locally:

    $ git clone
  3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

    $ make setup-venv
  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you’re done making changes, check that your changes pass flake8 and the tests

    $ make lint
    $ make test

    If the modification doesn’t affect code that configures and runs Galaxy - skipping a couple tests that will cause Galaxy and its dependencies to be downloaded results in a significant speed up. This subset of tests can be run with make quick-test.

  6. Commit your changes and push your branch to GitHub:

    $ git add .
    $ git commit -m "Your detailed description of your changes."
    $ git push origin name-of-your-bugfix-or-feature
  7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.

  2. The pull request should work for Python >=3.7. Check and make sure that the tests pass for all supported Python versions.


To run a subset of tests:

% make tox ENV=py37-unit ARGS='--tests tests/'

This will use Tox to run the specified tests using Python 3.7. ENV here can be used to specify different Python version (e.g. py36 or py37).

Even more granularity is also possible by specifying specific test methods.:

make tox ENV=py37-unit ARGS='--tests tests/'

tox can be used to run tests directly also (use . .venv/bin/activate to ensure it is on your PATH).

tox -e py37-unit -- --tests tests/

Tox itself is configured to wrap nose. One can skip Tox and run nosetests directly.

pytest tests/


Tox is a tool to automate testing across different Python versions. The tox executable can be supplied with a -e argument to specify a testing environment. Planemo defines the following environments:


Lint the planemo code using Python 3.7.


Lint the docs reStructuredText.


Lint the project Python docstrings (doesn’t pass currently).


Run the fastest unit tests (with least external dependencies) on Python 3.7.


Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05. Skip tests that are marked as redundant or that require a Galaxy client build.


Run tests that are marked as targeting a Galaxy branch and test against Galaxy’s dev branch.

Pre-commit Hooks

Planemo pull requests are automatically linted and tested using TravisCI. A git pre-commit hook can be setup to lint and/or test Planemo before committing to catch problems that would be detected by TravisCI as early as possible.

The following command will install a pre-commit hook that lints the Planemo code:

make setup-git-hook-lint

To also run the faster planemo tests, the following command can be used to setup a more rigorous pre-commit hook:

make setup-git-hook-lint-and-test