Hello all; I've been working again on the new directory structure and autoconf/automake build and posted an update at the same place as before: http://alpha.bioinformatics.org/bradstuff/index.html. The changes since yesterday are: 1. The INSTALL file has been updated with all the info about the current installation process. Please check it out and let me know if it makes any sense :-) 2. We are now byte-compiling (with optimization!) the .py scripts using James Henstridge's patches to automake. So now we are properly installing the python files--yippee! 3. I added the stuff I'm working on for wrapping some overflow code to be used in the definition layer. This is compiling for me, using gcc 2.95.2, but I'm really interested to hear if it compiles for anyone else, since this code will need to be able to compile for everyone to use piper in the future. Please let me know any errors you get, so I can try to figure this all out. If you get stuck badly on the compile and can't go any further, you can skip this part of the make (it isn't necessary to make anything work right now) by modifying dl/Makefile.am as follows: was -> SUBDIRS = modules scripts vflow now -> SUBDIRS = modules scripts and then running ./autogen.sh to revamp everything. As always, I'm looking forward to hearing from everyone about this. Toodle-loo! Brad