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From : https://doc.owncloud.org/server/9.0/admin_manual/maintenance/manual_upgrade.html

Manual ownCloud Upgrade

Always start by making a fresh backup and disabling all 3rd party apps.

php occ maintenance:mode --on

Back up your existing ownCloud Server database, data directory, and config.php file. (See Backing up ownCloud.)

in ownCloud-new dir: wget http:/..../owncloud-[version].tar.bz2 tar xjf owncloud-[version].tar.bz2

Rename your current ownCloud directory, for example owncloud-old. Rename ownCloud-new dir to ownCloud

Copy the config.php file from your old ownCloud directory to your new ownCloud directory.

If you are using 3rd party applications, look in your new owncloud/apps/ directory to see if they are there. If not, copy them from your old apps/ directory to your new one. Make sure the directory permissions of your third party application directories are the same as for the other ones.

Launch the upgrade from the command line using occ, like this example on CentOS Linux: php occ upgrade

sudo -u www-data php occ maintenance:mode --off

Reenable Caldendar and Contacts.