Bowtie

Description of program:

Versions:

Name: Bowtie 
Version: 2.2.3
Platform: x86_64
Category: Applications/Scientific
URL: http://bowtie-bio.sourceforge.net/index.shtml

Below is how to load the module into the software:
Module loading reference

Sample SLURM runtime script:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=4gb
#SBATCH --time=01:00:00

# Set paths or load appropriate modules
module load bowtie2

# Set $TMPDIR variable
export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID

# Set application variables
export SCR=${TMPDIR}

# Set auxiliary variables
INPUT_DIR="input"
INPUT_FILE1="lambda_virus"
INPUT_FILE2="reads_1.fq"
OUTPUT_DIR="output"
OUTPUT_FILE="eg1.sam"

# Create temporary directory
mkdir -p ${TMPDIR}

# Copy input data to directory indicated by $TMPDIR variable
cp ${SLURM_SUBMIT_DIR}/${INPUT_DIR}/* ${TMPDIR}

# Go to $TMPDIR directory
cd $TMPDIR

# Perform calculations
bowtie2 -x ${INPUT_FILE1} -U ${INPUT_FILE2} -S ${OUTPUT_FILE}

# Footer
cat << EOF
-------------------------------------------------------------------------------

End of calculations [$(date)].

-------------------------------------------------------------------------------
EOF

# Finish calculations, copy contents of $TMPDIR/output directory to 
# directory from which the job was queued.
mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR}
cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/

# Clear working directory
rm -rf $TMPDIR

The files that should be in the input directory are below:
File:Bowtie input.zip