use my_db;
flush tables [list of MyISAM tables];
lock each MyISAM table for read: `lock table <MyISAM table> read`

MYSQL_USER=root
MYSQL_PASS=rootpassword
MYSQL_CONN="-u${MYSQL_USER} -p${MYSQL_PASS}"
CONVERT_SCRIPT=/tmp/ConvertMyISAMToInnoDB.sql
echo "SET SQL_LOG_BIN = 0;" > ${CONVERT_SCRIPT}
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
SQL="${SQL} FROM information_schema.tables WHERE engine='MyISAM' AND"
SQL="${SQL} table_schema NOT IN ('information_schema','mysql','performance_schema')"
mysql ${MYSQL_CONN} -ANe"${SQL}" > ${CONVERT_SCRIPT}
less ${CONVERT_SCRIPT}