Ricardo Wurmus writes:

> Since bowtie's Makefile explicitly checks that the system it is built on
> is x86_64 building on MIPS and i686 should be disabled.  (See bug#19708
> for discussion.)
>
> This is what the attached patch does.

Please disregard the above patch and consider the attached one instead,
which also patches the Makefile (with an upstream patch for the next
release) to fix the build errors on x86_64.

~~ Ricardo