Place for birds with eggs by railway, all right for nesting (7)
I believe the answer is:
rookery
'place for birds' is the definition.
'eggs by railway all right for nesting' is the wordplay.
'eggs' becomes 'roe' (I've seen this before).
'by' says to put letters next to each other.
'railway' becomes 'ry' (abbreviation for railway).
'all right' becomes 'ok' ('ok' can be a synonym of 'all right').
'for nesting' is an insertion indicator ('nest' can mean to fit one object into another).
'roe'+'ry'='roery'
'roery' placed around 'ok' is 'ROOKERY'.
'with' is the link.
(Other definitions for rookery that I've seen before include "Breeding-place of birds, penguins, seals" , "Seal, penguin, colony" , "Noisy bird colony" , "Nesting-place" , "Lofty breeding-place" .)