> The file that Gift is producing is already an html file and there's
> already an html datatype in Galaxy by default.  The output file in
> question just invokes remote javascript libraries inside <script> tags,
> and this seems to be tripping up Galaxy's data viewer.  

Setting up relative paths to images and scripts inside your HTML output should 
work; this is done in FastQC and other similar tools.

> We've tried downloading and referencing the
> javascript libraries in /static/js as well.

This should work as well and is the approach used by the rGenetics tools, but 
the path you want is /static/scripts/ Note that Galaxy already has many jQuery 
libraries in /static/scripts/libs/jquery, which could simplify development.

> I know that the new visualization platform in Galaxy uses a lot of
> external javascript libraries like D3Š does anyone know how that is being
> handled differently?

For now, the viz framework is a different code base that's not relevant for 
displaying datasets.

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