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There are modules written for database backup and files backup, but what I want is a complete backup to Amazon S3 or other cloud platforms, for both the data, and the sites. Currently as it stands, I have to separately and manually backup the two.

Is there any module/tool/already-written-script that allows me to do that?

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This is more dependent on your hosting rather than Drupal; but if you're using EC2, you can use EBS which automagically stores your data in S3.

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