Greg von Kuster, Daniel Blankenberg
Penn State / Galaxy Team
The Galaxy Tool Shed enables sharing of Galaxy tools, proprietary datatypes, exported Galaxy workflows, data, and more (collectively: “Galaxy Utilities”) across the research community with ease. Tools can be automatically discovered and installed into a local Galaxy environment in real time, and they can easily be deactivated or uninstalled when they are no longer needed. Here, we demonstrate newly developed features of the Galaxy Tool Shed.
Although the Tool Shed has allowed multiple tool versions to be installed at a single time, the Tool Shed now simplifies the process of ensuring that underlying 3rd party tool dependencies are met by providing the option of automated download and installation of underlying dependencies.
A complex repository dependency system has also been implemented. This system allows a Tool Shed repository to depend on any number of other Tool Shed repositories. This powerful feature has formed the basis for the continuing development of best practices for designing Galaxy Tool Shed Utilities.
While the GUI for installing Tool Shed utilities continues to be improved, a RESTful API has been developed to allow automatic scripted installation, greatly simplifying the process of bootstrapping a new or existing Galaxy instance with many individual tool suites.
To ensure the quality of the Tool Shed and the available contributed Utilities, new testing frameworks have been developed for not only testing the Tool Shed feature-set, but also automatic functional verification and testing of community contributions. Additionally, the Intergalactic Utilities Commission (IUC) has been established to provide expert feedback on community contributions.