I have VPS and I don`t know the best way. /var/www/my_app or /home/user/www/my_app or something else? Which alternate is better?

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You can put you app wherever you want. That being said if you chose /var/www... then you will be using a path that is fairly common. One of the benefits of this is that many tutorials and other documentation commonly use /var/www so it's easy to follow them and relate to your own website/app.

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maybe create special user "deploy" and put /home/deploy/www? – mystdeim Apr 9 '11 at 12:59
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