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Or you could do like I did.
Owncloud and COPS are installed in the same server.
On my server, owncloud is installed in /var/www/owncloud. Cops is installed in /var/www/cops
I've created a user called cops in owncloud and with that user I have a directory called Calibre (which is synchronized with my Calibre library).
With that configuration, I just had to configure COPS's config_local.php like that :
$config['calibre_directory'] = '/var/www/owncloud/data/cops/files/Calibre/';
That's really easy to handle.
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