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I would prefer to work with the latest version, but unfortunately till that is available i want to find if theres some way to work with the available tools.
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If you are running Quartus 10.0, and compiling for the DE4, then you must already have a subscription license. In that case, just install the newer version of Quartus.
I did some tests on the Qsys stuff in this thread:
http://www.alteraforum.com/forum/showthread.php?t=35678 Using the 11-series of tools. I haven't tried using PCIe with 12.x or 13.x, but the PDF describes the sequence used to create the IP cores, so it should be sufficient for you to create an example for the DE4.
Cheers,
Dave