A belated response that I'll answer for others on Splunkbase.
To summarize:
If you use S3 as your storage, setting up Hadoop to use the data is up to you. You can use Hadoop in EC2, or EMR. (keep in mind you need to archive in CSV format; only Splunk can understand the Splunk Bucket format)
In order to setup Shuttl for Amazon S3, you provide a URI indicating the backend. Inside, $SPLUNK_HOME/etc/apps/shuttl/conf you'll see archiver.xml. In that file, you'll edit the archiverRootURI to have a value of the form: s3:// : @ /
In addition, keep in mind that though "s3n" will work as well for Shuttl, you will need to keep in mind the limitation of file size. In general, it's safest to use "s3".
See the Quickstart guide for more information: https://github.com/splunk/splunk-shuttl/wiki/Quickstart-Guide
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