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For ActiveMQ server to run properly some basic system variables must be set. These variables define how much memory broker will have, SSL, logging, JAAS options and similar. Prior to version 5.11.0 these parameters were configurable in activemq script itself. You could use setup command to create additional system wide scripts to configure the broker.
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Since 5.11.0, all configuration variables are moved to the new env script, so that they can be easily configured at one place. This script can be copied to /etc/default/activemq or $HOME/.activemqrc to provide system-wide settings, so the setup command has been removed. System variables set in the environment will take precedence.