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Contributing

This document describes how to contribute to this repository. Pull requests containing bug fixes, updates, and extensions to the existing tools and tool suites in this repository will be considered for inclusion.

What not to contribute

  • New tools.

    If one wishes to add new tools to the Galaxy tool shed - it is probably best to publish them under a personal or organizational account. Under exceptional conditions and if the tools are of sufficient quality and broad appeal - it may be worth discussing including them in the Galaxy IUC repository. This repository however is mostly for older, existing tools pre-dating the IUC.

    There are nonetheless many existing tools here for very popular bioinformatics programs - extensions or bug fixes for these tools will certainly be considered.

  • Purely stylistic fixes.

    This repository contains many old wrappers that are likely infrequently if ever used. If you are not actively planning on extending a tool and have not encountered a bug - it is probably best to just leave the tool alone so we can focus on newer more contemporarily useful tools.

    If you are looking for a good way to contribute to Galaxy - consider the ideas in this Trello card.

How to Contribute

  • Make sure you have a GitHub account

  • Make sure you have git installed

  • Fork the repository on GitHub

  • This repository was derived from mercurial repositories in the tool shed and may contain certain artifacts that should be fixed before committing new functionality in such files. These include:

    • The tool shed will automatically assign certain fields in tool_dependencies.xml during upload - these fields should be left blank in this git repository.

    • Related tools may be broken out into individual folders with duplicated wrapper scripts or macro files - these should be moved to a common location in this repository and symbolically linked to the original locations prior to modification.

  • Make the desired modifications - consider using a feature branch.

  • Make sure you have added the necessary tests for your changes and they pass.

  • Open a pull request with these changes.