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Feb 4, 2015: Getting IGV to work on Apple Macintosh computers is becoming increasingly difficult as Apple ramps up Java application security. Here is the current work around for OS/X Mavericks.
First, make sure you are getting the IGV launcher file downloaded. It should be in your Downloads folder and be named 'igv.jnlp' or some variant like 'igv-1.jnlp'. If you can find the jnlp file, then you need to allow it to launch IGV in your Java security settings:
(1) Open System Preferences on your Mac.
(2) Select Java (bottom row). The Java Control Panel opens in a separate window.
Select the Security tab, then click on the "Edit Site List..." button to pop up the Exception Site List window.
(3) Click on the Add button in the Exception Site List window.
(4) Under Location, enter https://s3.amazonaws.com, then press the OK button to add the security exception.
(5) Press OK on the Java Control Panel to finalize the security exception.
Now you should be able to go to the Downloads folder and launch IGV with the igv.jnlp file.