Another tip that could be useful: in the guide there are some problems with relative versus absolute paths, particularly in the parameters passed on to the different scripts. For example, in the tuning section the command to be run is this:
If that looks scary it's a sign of good mental health. I've started by doing a symlink for the scripts-YYYYMMDD-HHMM directory called simply scripts so it looks a bit tidier. But in any case,
nohup nice tools/moses-scripts/scripts-YYYYMMDD-HHMM/training/mert-moses.pl work/tuning/nc-dev2007.lowercased.100.fr work/tuning/nc-dev2007.lowercased.100.en
tools/moses/moses-cmd/src/moses work/model/moses.ini --working-dir work/tuning/mert --rootdir /home/jschroe1/demo/tools/moses-scripts/scripts-YYYYMMDD-HHMM/
--decoder-flags "-v 0" >& work/tuning/mert.out &
to finally make the script work I had to add an explicit indication for the mert directory in that already overcrowded command line.