This question asks for pointers about generating JtR rulesets, but the OP states
I understand how to use it to make various permutations from a given wordlist
Could someone please explain that? From the documentation, it seems as though REGEX mode, MASK mode, and Wordlist mode all permit this.
But how to generate a rule that contains permutations of a certain word (suffixes, prefixes, 1337speak)?
This is a solution for suffixes and prefixes for a given fixed, without 1337speak.
Using MASK mode, you give parameters on the command line. If the known word part is barquux and you need to suffix 3 characters and prefix 2, all of them digits, use
john -mask=?d?dbarquux?d?d?d -min-len=9 -max-len=14 file_to_crack
For mask options, see the MASK mode documentation file.
If you would like John the Ripper (JtR) to have permutations of certain words from a wordlist (let them be in the file dict.txt) with 1-printable-ASCII-character suffix, 1-printable-ASCII-character prefix, 1337speak, with the MASK attack and Hybrid Mask, you could use commands like this:
john.exe --wordlist=dict.txt --rules=All --mask=?w?a hash.txt
john.exe --wordlist=dict.txt --rules=All --mask=?a?w hash.txt
The 3l33t rules are included in the rules of the above commands.