example.qsub

#!/bin/bash -l

# Lines beginning with #$ are passed to qsub as options.

# Project, which may have dedicated resources
#$ -P mylab

# Name of job
#$ -N vntrseek_example

# File to receive standard output
#$ -o test.out

# File to receive standard error
#$ -e test.err

# Email for notifying of events
#$ -M your_email@domain.com

# Events to notify for; (b)egin, (e)nd, (a)bort
#$ -m bea

# Request particular resources
# project dedicated resources
#$ -l buyin
# 30 hours (h)ard limit (r)un (t)ime
#$ -l h_rt=30:00:00

# Multiprocessing environment, 8 cores
#$ -pe omp 8

# load tools into envionment, you'll likely need to change this
module load samtools perl sqlite3

# change this
install=/path/to/vntrseek/install/folder

reference=/path/toi/reference/prefix

# minimum run options
$install/vntrseek.pl 100 --RUN_NAME example_run
$install/vntrseek.pl 0 20 --RUN_NAME example_run --INPUT_DIR example_data/ --REFERENCE $reference

# or if you'd like to use a config
# $install/vntrseek.pl 100 --CONFIG example.cnf
# $install/vntrseek.pl 0 20 --CONFIG example.cnf