STAR through module rcbio/1.3.3

Start an interactive job, with a walltime of 2 hours, 2000MB of memory.

srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash

Create a working directory on scratch and change into the newly-created directory. For example, for user abc123, the working directory will be

mkdir /n/scratch/users/a/abc123/star
cd  /n/scratch/users/a/abc123/star

Copy the example bowtie2 bash script:

module load gcc/6.2.0 python/2.7.12 rcbio/1.3.3
cp /n/app/rcbio/1.3.3/bin/star.sh ./

Now you can take a look and modify the software options as needed.

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.

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

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

HMS IT RC O2