Developing Galaxy tools for the Tool Shed
The Galaxy Tool Shed enables sharing of Galaxy utilities across the Galaxy community. A misconception of the Galaxy Tool Shed is that it is a source code repository for developing Galaxy tools. It is not!! If you treat the Tool Shed as a source code repository for your tools while they are in development, you will undoubtedly experience unexpected (and potentially undesirable) behavior.
The primary intent of the Tool Shed is for sharing functionally correct Galaxy tools, workflows and other useful Galaxy utilities. Galaxy tools are generally developed within a local Galaxy environment, proven to be functionally correct within that environment, and then uploaded to a public Tool Shed for sharing. Local development Tool Sheds may be beneficial components of a Galaxy tool development environment.
With a couple of exceptions, support for tool features are restricted to the Galaxy framework. The following links refer to pages that describe those exceptions.
Building Tools with Dependencies in the Same Repository
Building Tools with Dependencies in Separate Repositories
Structuring Tools in Your Repository
Recipes for Installing and Compiling Packages Required by Galaxy Tools