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I am quite new and somehow I crashed my phpMyAdmin website. It can't be displayed without errors after changing the port of it once. So does it have any effect on my databases when I reinstall my phpMyAdmin? I guess it will not change anything since it doesn't come bundled with MySQL, but I want to be sure.

Can I simply uninstall and re-install without losing any data from MySQL databases?

I use an Ubuntu 12.04 server.

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There will be no impact on you running database(s) as phpMyAdmin is just a management interface.

Use: apt-get remove phpmyadmin

Remove /etc/phpmyadmin config directory and check your /etc/apache2/sites-enabled/ vhost files.

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Yes, phpMyAdmin is just another piece of software and MySQL doesn't depend on it to run.

But maybe you'd better try to debug and resolve this issue? Nothing stops you from nuking your phpMyAdmin again. Can you at least post some logs, include some config samples?

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