Generalising Grid Engine qsub job file for multiple programs and input file names

I am using Grid Engine on a Linux cluster. I am running many jobs with different programs and different input files. I don't want to create multiple specific job scripts for each pair of program and input file. Instead I want to be able to specify the program name and the input file on the qsub line. Therefore I can use qsub job.sh Where job.sh takes two arguments. This works fine. But there is another twist: my programs are located in a very very long directory which I don't want to type every time I submit a job - so aliases are an obvious choice. So I want to do something like qsub job.sh I initially set the alias in my .bashrc but was getting the error: : command not found So I set the alias in submit.sh. But I am getting the same error. Thoughts on how can I can get the command qsub job.sh $1 $2 to accept aliases also?