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module load gcc/6.2.0 python/2.7.12 rcbio/1.1
cp /n/app/rcbio/1.1/bin/star.sh ./

Now you can modify the options as needed. 

nano star.sh

To test the pipeline run the following command. Jobs will not be submitted to the scheduler. Here -r is the reference, -l is the read length. 

runAsPipeline "star.sh -r hg38 -l 100" "sbatch -p short --mem 6G -t 10:0 -n 1" noTmp

# this is test run

To run the pipeline. Here -r is the reference, -l is the read length. 

runAsPipeline "star.sh -r hg38 -l 100" "sbatch -p short --mem 6G -t 10:0 -n 1" noTmp run 2>&1 | tee output.log

# notice here 'run 2>&1 | tee output.log' is added to the command

To understand how 'runAsPipeline' works, please visit: Run Bash Script As Slurm Pipeline through rcbio/1.1