Running a canned program (cellranger)
======================================


.. code-block:: bash

    #!/bin/bash

    #$ -cwd
    #$ -l h_rt=8:00:00,h_data=2g
    #$ -o Stdout.$JOB_ID
    #$ -e Stderr.$JOB_ID
    #$ -j n
    #$ -m bea

    # Use system-wise modules
    source /u/local/Modules/default/init/modules.sh
    module load cellranger

    # Run program
    cellranger count --id=normal --transcriptome=$PATH --fastqs=$PATH ....