FastTree doesn't honour --num_threads due to OpenMP vars

[tseemann]

FastTree uses OpenMP and respects the $OMP_NUM_THREADS variable.

Can you override that variable if the user specifies --num_threads ?

It should still respect the overall $OMP_THREAD_LIMIT variable.

[douglasgscofield]

I would add that if the build command at http://www.microbesonline.org/fasttree/#Install is followed, the MP-enabled FastTree executable is FastTreeMP, and the non-MP executable is FastTree. Those are the names I have given the executables in our site module.

[tseemann]

To control this in Nullarbor I just run it as env OMP_NUM_THREADS=$threads FastTree ...

[nickjcroucher]

Gubbins should now use the MP-enabled version by default in bf3bd21.