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 $ perl mycode.pl file1.txt param1 param2 > param_set1.out 
 $ perl mycode.pl file1.txt param3 param4 > param_set3.out
 $ perl mycode.pl file1.txt param4 param5 > param_set4.out

 $ cat param_set1.out param_set3.out param_set4.out  > final.out

#!/usr/bin/bash

cd ~/some_dir
perl mycode.pl $1 $2 > ~/some_out_dir/param_set$1.out

$ qsub runcode.sh param1 param2
$ qsub runcode.sh param3 param4
$ qsub runcode.sh param5 param6