Lately I've tried compiling the latest version of bwa on github in CentOS 7.2 on ppc64 but I get stuck on an x86_64 dependency (emmintrin.h). I found that this header file is specific to SSE2 instructions on x86 machines.
Roughly 2 years ago I was able to compile bwa on my PowerMac G5 so I'm not sure what changed since then that made bwa require x86_64.
This is probably something worth asking on the bwa mailing list, possibly combined w/ tagging this report with 'bwa'
Ah yes, didn't realize this pings someone :)