Use innobackupex with backupninja. Place under /usr/share/backupninja/innobackupex

innobackupex

# -*- mode: sh; sh-basic-offset: 3; indent-tabs-mode: nil; -*-
# vim: set filetype=sh sw=3 sts=3 expandtab autoindent:
#
# duplicity script for backupninja
# requires duplicity >= 0.4.4, and >= 0.4.9 when using a custom tmpdir.
#


######################################
# backupdir: Where to backup to
# incremantal: yes/np crate incremental backups
# full_on: Iso 3 Char Day of Week on which a new full backip should be made.
# max_age: Max Age in days of how long a backup is stored.
# nicelevel: nice lebel
# options: custom options to pass
##############################

getconf basebackupdir /var/backups/mysql/base
getconf incrbackupdir /var/backups/mysql/incr
getconf incremental yes
getconf full_on mon
getconf max_age 14
getconf nicelevel 0
getconf options

# authentication:
getconf user
getconf dbusername
getconf dbpassword
getconf configfile /etc/mysql/debian.cnf

### COMMAND-LINE MANGLING ######################################################

### initialize $execstr*
execstr_precmd=
execstr_command=
options="$options --user=$user --password=$dbpassword"

day_of_week=$(date +%a)

# Check base dir exists and is writable
if test ! -d $basebackupdir -o ! -w $basebackupdir
then
  fatal "$basebackupdir does not exist or is not writable"
fi
# check incr dir exists and is writable
if test ! -d $incrbackupdir -o ! -w $incrbackupdir
then
  echo "$incrbackupdir does not exist or is not writable"
fi

if [ -z "`mysqladmin $USEROPTIONS status | grep 'Uptime'`" ]
then
  fatal "HALTED: MySQL does not appear to be running."
fi

debug "Check completed OK"

###Check for empty backupdir, if so force full backup
if [ "$(ls -A $basebackupdir)" ]; then
   incremental=$incremental
else
   incremental="no"
fi

latest=`find $basebackupdir -mindepth 1 -maxdepth 1 -type d -printf "%P\n" | sort -nr | head -1`

### Incremental or full backup mode
# If incremental==yes, use the default duplicity behaviour: perform an
# incremental backup if old signatures can be found, else switch to
# full backup.
# If incremental==no, force a full backup anyway.
if [ "$incremental" == "no" ]; then
   execstr_command="$basebackupdir"
else
   if [ "${day_of_week,,}" == "$full_on" ] ; then
      execstr_command="$basebackupdir"
   else
      latestincr=`find $incrbackupdir/$latest -mindepth 1  -maxdepth 1 -type d | sort -nr | head -1`
      if [ ! $latestincr ]
      then
         # This is the first incremental backup
         incrbasedir=$basebackupdir/$latest
      else
         # This is a 2+ incremental backup
         incrbasedir=$latestincr
      fi
      
      execstr_command="--incremental $incrbackupdir/$latest --incremental-basedir=$incrbasedir"
   fi
fi



### Backup command
debug "$execstr_precmd innobackupex $options $execstr_command"
if [ ! $test ]; then
   outputfile=`maketemp backupout`
   output=`nice -n $nicelevel \
             su -c \
                "$execstr_precmd innobackupex $options $execstr_command  >$outputfile 2>&1"`
   exit_code=$?
   debug $output
   cat $outputfile | (while read output ; do
                         if [ $exit_code -eq 0 ]; then
                            info $output
                         else
                            error $output
                         fi
                      done
   )
   if [ $exit_code -eq 0 ]; then
      info "innobackupex finished successfully."
   else
      fatal "innobackupex failed."
   fi
   rm $outputfile
   
   # Delete old bakcups
   info "Cleanup"
    for DEL in `find $basebackupdir -mindepth 1 -maxdepth 1 -type d -mtime +$max_age -printf "%P\n"`
    do
      echo "deleting $DEL"
      rm -rf $basebackupdir/$DEL
      rm -rf $incrbackupdir/$DEL
    done
fi




return 0