Unless you have special requirements (and assuming you’re an academic user), it’s highly recommended to just use the fragment server at http://www.robetta.org/ – it works with just the sequence, and saves a bunch of headaches in getting things set up.
If that’s not going to work for you, you may want to clarify what you’re trying to accomplish – what special restrictions, limitations, or requirements feed into your decision to make fragments locally. How are you intending to set up the Null_fragment protocol?
Note that it’s probably not productive to do fragment picking with “just” a sequence – you’ll want to bring in secondary structure prediction at least. Although that can be done by running external programs on your fasta sequence. (Getting those external files set up is most of the headaches of running the fragment picker locally.)
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