Yes, the Galaxy team is working on a JavaScript binding to the API, and one of the areas that we've done some work on is running tools. It's probably a little heavyweight if all your want to do is push datasets into Galaxy—HTTP posts to the API will work just fine—but it's useful if you want real integration between Galaxy and your Web application (JBrowse or otherwise), such as the ability to work with histories/datasets/tools/visualizations on the fly.

J.