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I found a bug/feature. I was able to create multiple databases without the need for my own dockerfile. I kinda abused the docker-entrypoint.sh. Below is a terminal session that shows how I did it
$ cat elist
MYSQL_DATABASE=one`; CREATE DATABASE IF NOT EXISTS two; CREATE DATABASE IF NOT EXISTS `three
MYSQL_ROOT_PASSWORD=pass
$ docker run -p 127.0.0.1:3306:3306 --env-file elist mysql
I'm not sure want to do with this information, but it works as a quick hack to get multiple databases.