jtag Daisy Chain compiler setting

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I need some information regarding a design, where if two devices are JTAG daisy chained e.g. Altera CPLD and SAM4E series microcontroller.

As far as the hardware and layout is concerned, I know how to daisy chain, however I dont know how can I tell the compiler to program SAM4E microcontroller and to IGNORE Altera CPLD.

Also I prefer to work with make files, is there a way I include that instruction in my Makefile so that when I issue "make program" it ignores Altera CPLD?

I thank you for your help.