#!/bin/bash -l
# don't forget '-l' option in above line
# it is critical to make the following
# lines starting with '#$' relevant and 
# 'module load' command available

#Specify project
#$ -P scv # replace with your own project_name

#Give the name to the job
#$ -N bowtie2_basic_example

#Send an email when the job is finished (or aborted)
#$ -m ae

#Join the error and output file 
#$ -j y

#Sepcify the version of bowtie
module load bowtie2/2.4.2

# run bowtie2-build to build index
cd ref
bowtie2-build NC_012967.1.fasta NC_012967.1

# go back to example root directory:
cd ..
# call bowtie2 command using relative path for the input/output parameters: 
bowtie2 -t -x ref/NC_012967.1 -1 data/SRR030257_1.fastq -2 data/SRR030257_2.fastq -S bowtie2_example_SRR030257.sam

# print out end message: 
echo "DONE!"