> Passing it back to Jeremy, there is also a Javascript wrapper around the
> tools API which might help:
> https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools.js

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.


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