1) Create a job-script myJobScript.sh

Job-script contains the HPC queue settings (queue name, log-files, email, ...) and the main tool command (e.g. echo, BLAST, bowtie2, ... )

Example job-script (text file) myJobScript.sh

#!/bin/bash

#$ -q std.q # queue name to which script will be submitted

#$ -N DemoScript # script name to be visible in the queue

#$ -o /my/new/project/log_output_$JOB_ID.txt # command output file in project path

#$ -e /my/new/project/log_error_$JOB_ID.txt # command error message file

#$ -M my.email.address@gmail.com # to get notifications about script status

#$ -m ea # send email in case of job end or abort(error)

#$ -pe smp 8 # number of required processors

# go to working directory

cd /my/new/project/

# run main tool command

echo "Hello from `hostname`!"


2) Submit the job-script

# submit a job-script ( add “myJobScript.sh” as new job to queue “std.q” )

qsub myJobScript.sh

# check status of all submitted jobs ( Is my job still waiting in queue or already running? )

qstat -f

# delete job ( remove an already submitted job-script by using the job-ID "12345" shown by "qstat -f" )

qdel -j 12345