The command to convert a single table from MyISAM to InnoDB looks like:
ALTER TABLE tablename ENGINE = INNODB;
This is described suscintly by Major.IO:
Kevin van Zonneveld goes further in his blog:
and provides some scripts to convert all tables instead of doing one at a time.
I like the following:
echo "SELECT CONCAT('SELECT \"',table_schema,'.',table_name,'\";ALTER TABLE ',table_schema,'.',table_name,'
AND engine = 'MyISAM'
AND table_schema NOT IN ('information_schema', 'mysql', 'performance_schema');" | \
mysql | grep -v CONCAT | mysql
This variation shows the table name before starting the conversion so I can see progress. The query output is pipped right back in to mysql to execute.