INSTALL

Most of the actions outlined below may be accomplished by simply running:
./setup.sh from within the PRFdb distribution.
One will still need to make a prfdb.conf and apache configuration to run a webserver,
as well as ./prf_daemon --setup_db

Required Software that isn't likely to be in your distribution:
rnamotif
pknots
nupack
hotknots
ViennaRNA

The list of required perl modules may be found in lib/MyDeps.pm
It makes an attempt to auto-install anything that is missing.
If it fails, you can run perl -MCPAN -e shell
then install 'missing_module' in order to get yourself squared away. 

Required Editing:
Set PRFDB_HOME in your apache configuration, check the file
apache/xprfdb.conf for more details
If you are running a web server you will also need to set
PRFDB_NAME and PRFDB_IP

Copy prfdb.conf.default to prfdb.conf
The fields for database_user, database_pass etc need to be changed.
Most other settings are fine by default, but you can change pretty much
anything from the configuration file if you desire.

Make sure that apache has libapreq running.  On a Debian installation this
may be done by symlinking /etc/apache2/mods-available/libapred to 
/etc/apache2/mods-enabled/

Make sure the $PRFDB_HOME/sessions symlink points somewhere real and is apache
writeable.

Finally:
Run ./prf_daemon --setup_db

You can test your installation with:
./prf_daemon --shell

If it worked, you can do a show tables and see all the initial tables.
At that point, you will likely want to import some sequences.
./prf_daemon --import needs to be documented...
but by default will take an NCBI accession and import that.