Generating SSH keys for 'apache' user
You may have to copy the root generated keys in the .ssh directory of your apache user.
Assuming the homedir of apache is /var/www (check /etc/passwd) and the named key is id_rsa-git :
mkdir -p /var/www/.ssh/cp /root/.ssh/id_rsa-git /var/www/.ssh/id_rsaNo need to copy the public key.
Note : by default the key used are id_rsa or id_dsa. You may change the name of the copied key to match this.
You may also change ownership of the id_rsa key and .ssh directory:
chown -R apache:apache /var/www/.sshchmod 0700 /var/www/.sshchmod 0600 /var/www/.ssh/id_rsa
Just posting the comment of @KitCarrau, under yvan's answer, that worked for me
sudo -u apache ssh-keygen -t rsa
for debian
sudo -u www-data ssh-keygen -t rsa
after this click Enter twice, to skip passphrase
also, it suggests to create the public/private keys in /var/www/.ssh directory, even if I had my www direcotry in /home/my_user/www, that is fine.