Using Nagios to monitor MySQL service availability is OK but certainly not slow queries.
I use a simple bash script which run every x seconds in crontab and scan processlist to capture queries running for more than 180 seconds. Hope it fits into your case aswell:
#!/bin/bash
[email protected]
count=0
# capture all running queries
echo "<TABLE BORDER=1><TR><TH>Queries running more than 180 seconds</TH></TR></TABLE>" > /tmp/long_running_queries.htm
mysql -uroot -ppassword -s -e "SELECT now(), ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO FROM information_schema.PROCESSLIST WHERE HOST not in ('%','localhost') AND COMMAND not in ('Sleep','Binlog Dump') AND TIME > 120;" > /tmp/all_running_queries.txt
echo "<TABLE BORDER=1>" >> /tmp/long_running_queries.htm
# store the output
while IFS= read -r ROW
do
count=$(($count + 1))
echo "<TR>" >> /tmp/long_running_queries.htm
echo "$ROW" >> /tmp/long_running_queries.htm
echo "</TR>" >> /tmp/long_running_queries.htm
done < /tmp/all_running_queries.txt
# if there are more than 2 long running queries then send the output from while loop above into mail
# else pruge the output
if (("$count" > "2"));
then
echo "</TABLE>" >> /tmp/long_running_queries.htm
Subject="$count SQL queries running for more than 180 Seconds"
Body="Some text"
echo $Body | mutt -a /tmp/long_running_queries.htm -s "$Subject" $Notify
else
echo "" > /tmp/long_running_queries.htm
fi