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Really sorry all, I had read the page several times then copied the command from the wrong text box. The non-sudo install worked fine, seems to have installed prerequisites, runs scheduled using:
sudo /home/ubuntu/calibre-bin/calibre/ebook-convert "/home/ubuntu/MyRecipev8.28v7.recipe" /home/ubuntu/ftp/MyBook.epub
Sorry for wasting your time kovidgoyal and thanks for the handy post on upgrades eschwartz and a little more understanding on the installer script.
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