WebUITheme Javascript

I am doing some dynamic URL creation in my loginFooter.html as part of a custom theme.  The problem I am having is that when I try to call a javascript function, my error console is telling me that it can not find the function (and obviously it is not getting called).  I have tried putting the function in a script block above the body tag as well as in the body tag.  Neither is making the function accessible.  The only way I can get the javascript I need to execute is by cramming it all in to the onclick event in my A tag.  Can someone tell me how I am supposed to be able to include a javascript block in the loginFooter.html file?