Ben,
You are right. I forgot to run:
> ./Setup --with-cd-hit=no --with-blast=no --with-spasm=no --with-procheck=no
since I have installed none of the external packages but modeller9.12.
However, when I run the demo under /demo, I get this error:
> python AddSeqMP.py --conf_file modpipe.conf --sequence_file test.fsa
**************************************************************************
Traceback (most recent call last):
File "AddSeqMP.py", line 17, in <module>
import modpipe.version
ImportError: No module named modpipe.version
**************************************************************************