Amazon S3 and ffmpeg

So we are setting up a file upload system for our web app. Files will be uploaded to Amazon S3, and videos need to be converted to ffmpeg. We have had problems with uploading of large files timing out, and it was suggested to us to use http://github.com/elcgit/s3-swf-upload-plugin for uploading directly to S3. This would fix the timeout, but then could I use ffmpeg to convert the file once it is on S3? If so, how would we accomplish this? If not, what would you suggest either for fixing the timeout issue or for processing video conversion? Essentially, what would be our best solution? Thanks in advance!

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