for x in $(echo "show tables;"| mysql --user=fartman --password=beer --host=10.11.12.13 --database=pet|grep -v Tables_in); do echo "alter table $x engine = innodb;" | mysql --user=fartman --password=beer --host=10.11.12.13 --database=pet;done
or:
http://www.linux.com/articles/46370
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