12345678:USE_BASES all 

# numbers before ":" below signify lane numbers
#use the following lines if you need to run ELAND
#otherwise omit

1:ELAND_GENOME /path_to_ELAND_files_genome_1 
24578:ELAND_GENOME /path_to_ELAND_files_genome_2

#use if you are going to run ELAND else omit

124578:ANALYSIS eland_pair     

#use if you only need sequence

36:ANALYSIS sequence_pair (for paired_end samples)
34:ANALYSIS sequence (for single end samples)

ELAND_SET_SIZE 4

WITH_SEQUENCE true