If your server is above 5.1.6 you can set the slow query log in the runtime itself. For which you have to execute this queries.
set global log_slow_queries = 1;
set global slow_query_log_file = ;
Or alternatively you can set the this options in the my.cnf/my.ini
option files
log_slow_queries = 1;
slow_query_log_file = ;
Refer: http://dev.mysql.com/doc/refman/5.1/en/server-system-variables.html#sysvar_slow_query_log_file