Heya, Andy Galaxy hasn't been designed to be loaded in an iframe yet. Currently, the javascript in Galaxy makes use of the window variable top - which points to the highest browser window in the DOM. There are many instances where we rely on both 'top' and the link target '_top' to control the iframes used inside the platform. In your implementation, top won't point to the Galaxy frame - but to the frame you've created. This can lead to pages/features that won't load (and fail silently unfortunately). We are currently working to remove our use of iframes within the platform which will help with embedding Galaxy into a frame. In the meantime, you may be able to alter those references to top to point to parent (which is context dependent) or to a named frame (naming the outer Galaxy frame and using that as a link target and replacement for top). Hope that helps. (with apologies to Andy for missing the mailing list in my first reply) On Thu, Oct 10, 2013 at 7:56 AM, Andy Saurin <andrew.saurin@univ-amu.fr>wrote:

Hi all,

I really can't understand why this should be, but in recent versions of Galaxy if you have a simple html page with an iframe embedding Galaxy, you loose the masthead (no login, workflow etc) and the history panel no longer works.

eg (newer Galaxy Versions)

<iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe> <iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe>

You can see the problems, whereas older versions of galaxy show no problems:

<iframe src="http://galaxy.berkeleybop.org:8080/" width="800px" height="600px"></iframe>

What could be causing this so that I can try to make amends?

Thanks Andy

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