Galaxy for Tool Developers


Every Galaxy is much defined by its tools. You can either use them as a user, install them as an admin, or contribute to the community by writing tools or preparing them for use with Galaxy as a tool developer.

Common Terminology

  • Wrapper or tool definition file: The XML file that describes to Galaxy how the underlying software works, thus allowing Galaxy to execute the software in the right way.
  • ToolShed repository: Tools in ToolShed are stored in versioned code archives. The ToolShed uses Mercurial as the platform of choice for this purpose.
  • Utility: Any component that can be uploaded to the ToolShed and installed into other Galaxy instances for general or specific analyses.
  • Workflow file: A JSON file describing steps in an analysis, which can be used to reproduce the analysis on another Galaxy instance.
  • IUC: Intergalactic Utilities Commission (read more).

Writing tools

Tools are written in XML language following the Galaxy tool schema. We encourage you to submit your finished tools to the Tool Shed.

Please use Planemo for both tool development (see the documentation) and publishing to the Tool Shed. We heartily recommend you use it together with the best practices for Galaxy tool development by the IUC. The IUC also provides tool developers with advice and guidance.

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