A .js file is not executed directly from the URL bar. Could you describe how you want to run it? For example, if you want to inject the script into the current page or have it operate on the current page, you could try saving it as a bookmarklet. To do that:

Right-click a blank area of the Bookmarks Toolbar and choose New Bookmark.

In the location, type or paste javascript: and then paste the script. At the end of the script, add void 0; (if necessary, add a semicolon before it so it is separated from the pasted script).

Give your bookmarklet a handy name then click Add.

Thank you for tip. Based on it, I was able to investigate a problem little deeper.

It looks like a browser behaviour differs between workstations and I don't have a clue why (both have FF 15.0.1). On a http://markup.io page, there is a area which says "Drag to a bookmarks bar".

Browser on one workstation shows it as a link to http://api.markup.io/bootstrap.js?v=1&

Other browser shows it as a javascript:...content here...;

It works if I paste javascript into a link as you stated or if I make a bookmark using the other workstation. But I am curious: what setting of my workstation is responsible of showing a link rather than actual javascript? I would like to avoid such problems in the future.

UPDATE: It was a Redirect Cleaner add-on which made links appear in such way. I did disable all add-ons when I was searching for reasons why bookmark is not working, but it was AFTER I created the invalid bookmark.