iOS only supports video streaming over the HTTP protocol, unlike Flash where you can use RTMP. A configuration example how to configure JWPlayer using a HTML5 fallback solution can be found in the documentation.
However, you need to keep care of these lines:
'provider': 'rtmp',
'streamer': 'rtmp://rtmp.example.com/application',
'file': 'sintel.mp4'
As said, iOS only supports streaming over HTTP, so you would need something like:
'provider': 'http',
'streamer': 'http://rtmp.example.com/application',
'file': 'sintel.mp4'
Of course your streaming server must support streaming over HTTP as well.
EDIT
In order to setup your JWPlayer in fancybox you can use the methods as usual. There is nothing special using Fancybox and JWPlayer together.
HTML
<div class="video_popup">
<div id="mediaplayer">Here the player will be placed</div>
</div>
Javascript (adapted from your question)
$(document).ready(function() {
$(".video_popup").fancybox({
fitToView: false, // to show videos in their own size
scrolling: 'no', // don't show scrolling bars in fancybox
afterLoad: function () {
// get dimensions from data attributes
var $width = $(this.element).data('width');
var $height = $(this.element).data('height');
// now, use JWPlayer to setup the player instead of embedding Flash
jwplayer('mediaplayer').setup({
// configuration code as in the documentation
});
}
});
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