To use the sqlite data bases instead of the text files you need to have the sqlite and boost libraries available. If they were available when the configure script was run the extension should have been compiled automatically. 

One needs to set the following options:

{{{
USE_DB yes
ASSEMBLY_DB_PATH /the/path/assembly.sqlite
TREES_DB_PATH /the/path/trees.sqlite
CUT_DB_PATH /the/path/cuts.sqlite
RAT_DB_PATH /the/path/rationals.sqlite
PARENTS_DB_PATH /the/path/parents.sqlite"
PARTIALS_DB_PATH /the/path/partials.sqlite"
}}}