Graduate set up software program for religious leader (5)
I believe the answer is:
abbot
'religious leader' is the definition.
(head of an abbey)
'graduate set up software program' is the wordplay.
'graduate' becomes 'BA' (someone with a Bachelor of Arts degree).
'set up' is a reversal indicator (in a down clue, letters go up).
'software program' becomes 'bot' (bot can mean an autonomous computer programme).
'ba' written backwards gives 'ab'.
'ab'+'bot'='ABBOT'
'for' acts as a link.
(Other definitions for abbot that I've seen before include "Head of a community of monks" , "meeting Newton in Devon" , "chap who'll be over order?" , "Head monk" , "Head of group of monks" .)