yep
added more options
ok
more options added
more options added
lots of oo stuff
handle database exception error from duplicate entries
bunch of changes to file transfer
tracked down some more issues with hard-coded path names
tracked down some more weird stuff
tracked down some more weird stuff
fixed issues with hmm and staging
updated documentation and blast db generation step
fixed some of my extra-fancy die statements back to regular ones, so the line numbers would be printed correctly
some more things
fixed remote transfer bug
fixed problems that turned out to be in never-used code, oh well
fixed the "could not find build_remote_lastdb_script.pl"  error
fixed the "fixed run_remote_search_handler not getting sent over the wire to the remote machine
fixed the directory-already-exists problem. still running into the "bulk loaded 0 orfs" problem though