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I have a one-click Wordpress install as part of my services. After install I want to show my clients a set of themes so they can choose one and their pages will start working without any configuration needed. The problem is I need to know how to change the theme from an external (PHP) application, perhaps accessing directly to the database or to one of the installation files.

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Take a look at the options table:

$opt_table = "{$GLOBALS['wpdb']->prefix}_options";
$parent_theme = $opt_table + template;
$child_theme = $opt_table + stylesheet;
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