To do a quick test-run, just issue (from this directory) the command:

perl emacc2.pl --source en --target ro --input test\doclist-en.txt --input test\doclist-ro.txt --output test-alignment.txt

In Windows, be sure to configure the file 'cluster.info' and 'emaccconf.pm' first! Especially if you have a lot of documents to align!
In Windows it is advisable to run EMACC under Cygwin.

For more details, please read ACCURAT D2.6 deliverable, Version 2.