In reply to deepak_infy:
It looks like you are mixing two different things, reset_phase and reset_sequence.If you have a reset_sequence and a configuration_sequence you can run them in the run_phase in a serial order:
In run_phase you are executing:
(1) reset_sequence
sequence1
(2) configuration_sequence
sequence2
(3) link training sequence
sequence3
In this case you do not need the reset_phase and the configuration_phase.