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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 D3? 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.

Best, J.

Thanks Jeremy, we'll give this a shot. -Andrew -- Andrew Stewart Office of Research Information Services (ORIS), Office of the Chief Information Officer (OCIO), Smithsonian Institution 202-633-2840 On 7/25/13 12:00 PM, "galaxy-dev-request@lists.bx.psu.edu" <galaxy-dev-request@lists.bx.psu.edu> wrote:

...

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 D3? 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.

Best, J.