Galaxy tool development

Tool development workflow (from GCC2014):

1. create a new Github repo or clone an existing tool from Github
2. upload to a local tool shed
3. install into a local Galaxy instance from the local tool shed for development/testing
4. upload to the test tool shed
5. install into a dev Galaxy instance for testing
6. upload to the main tool shed
7. install into a prod Galaxy instance

Notes:

• use capsules to import tools into the main tool sheds from a local tool shed
• there is support for dependency definitions across tool sheds via omitting the toolshed and/or the changeset_revision attribute in dependency definition tags: <repository name="molecule_datatypes" owner="test" /> (example: tool dependencies for tophat2)
• the dependency definition file is automatically altered to include these attributes and values at prior to it being committed to the tool shed repository in the changeset
• dependencies for workflows cannot be specified across tool sheds (e.g., must use tools from the dev tool shed as dependencies for workflows in the dev tool shed)

Resources:

• Advanced Galaxy tool development
• Example of a well-developed & tested Galaxy tool
• Galaxy tool xml syntax
• Add a Galaxy tool Tutorial
• Galaxy Intergalactic Utilities Commission Standards and Best Practices
• Hosting a Local Galaxy Tool Shed for Developing Galaxy Tools
• Planemo: command-line utilities to assist in building tools for the Galaxy project (Github)
• More things I done learned about Galaxy tool development
• Galaxy tool sheds