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Contributing

Galaxy welcomes new development! This document briefly describes how to contribute to the core galaxy project - also checkout our 2013 Galaxy Community Conference presentation on the topic (video, presentation). For information on contributing more broadly to the Galaxy ecosystem and a deeper discussion of some of these points - please see the Develop section of the Galaxy Wiki.

Before you Begin

If you have an idea for a feature to add or an approach for a bugfix, it is best to communicate with Galaxy developers early. The most common venues for this are GitHub issues and the Galaxy and Tool Shed Trello boards. Browse through existing GitHub issues and Trello cards and if one seems related, comment on it. We also maintain a card with links to smaller issues we believe would make the best entry points for new developers. Galaxy developers are generally available via IRC and on the development mailing list.

Reporting a new issue

If no existing Galaxy issue/Trello card seems appropriate, a new issue can be opened using this form.

How to Contribute

  • All changes to the core galaxy project should be made through pull requests to this repository (with just two exceptions outlined below).

  • If you are new to Git, the Try Git tutorial is a good places to start. More learning resources are listed at https://help.github.com/articles/good-resources-for-learning-git-and-github/ .

  • Make sure you have a free GitHub account.

  • Fork the galaxy repository on GitHub to make your changes. (While many Galaxy instances track galaxy-dist, active development happens in the galaxy GitHub repository and this is where pull requests should be made). To keep your copy up to date with respect to the main repository, you need to frequently sync your fork:

      $ git remote add upstream https://github.com/galaxyproject/galaxy
  $ git fetch upstream
  $ git checkout dev
  $ git merge upstream/dev

  • Choose the correct branch to develop your changes against.

    • Additions of new features to the code base should be pushed to the dev branch (git checkout dev).

    • Most bug fixes to previously release components (things in galaxy-dist) should be made against the recent release_XX.XX branch (git checkout release_XX.XX).

    • Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or without patches) to [email protected] . The Galaxy core development team will issue patches to public servers before announcing the issue to ensure there is time to patch and highlight these fixes widely. We will provide you credit for the discovery when publicly disclosing the issue.

  • If your changes modify code - please ensure the resulting files conform to Galaxy style guidelines.

  • Galaxy contains hundreds of tests of different types and complexity and running each is difficult and probably not reasonable at this time (someday we will provide a holistic test procedure to make this possible). For now, please just review the running tests documentation and run any that seem relevant. Developers reviewing your pull request will be happy to help guide you to running the most relevant tests as part of the pull request review process and may request the output of these tests. You can run the continuous integration tests locally using tox, example: tox -e py27-lint,py27-unit.

  • Commit and push your changes to your fork.

  • Open a pull request with these changes. You pull request message ideally should include:

    • A description of why the changes should be made.

    • A description of the implementation of the changes.

    • A description of how to test the changes.

  • The pull request should pass all the continuous integration tests which are automatically run by GitHub using e.g. Travis CI.

  • Your pull request will be handled according to some rules.

A Quick Note about Tools

For the most part, Galaxy tools should be published to the Tool Shed and not in this repository directly. If you are looking to supply fixes for migrated core tools that used to exist in this repository - please checkout the tools-devteam repository on GitHub.

More information about tool development can be found on the wiki.