MySQL - Convert tables from MyISAM to InnoDb

Convert All Tables From MyIsam To Innodb

Run this from linux to generate a script called MyISAM_To_Innodb.sql.  This script can then be run from within mysql command line using source and pointing to the script.
To convert all tables for all databases in an instance:
mysql -h... -u... -p.... -A --skip-column-names -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;') InnoDBConversionSQL FROM information_schema.tables WHERE engine='MyISAM' AND table_schema NOT IN ('information_schema','mysql','performance_schema') ORDER BY (data_length+index_length)" > MyISAM_To_InnoDB.sql
To convert all tables for a specified database:
mysql -h<hostname> -uroot -p<password> -S <socket path and file> -A --skip-column-names -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;') InnoDBConversionSQL FROM information_schema.tables WHERE engine='MyISAM' AND table_schema = '<database name>' ORDER BY (data_length+index_length)" > MyISAM_To_InnoDB.sql
The above commands can be modified for other purposes such as OPTIMIZE TABLE for reindexing.