Samtools

Program description:
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments Versions:

Name: Samtools
Version: 1.2
Platform: x86_64
Category: Development/Libraries
URL http://samtools.sourceforge.net/
Provides: samtools, bcftools

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 samtools

# Set the $TMPDIR variable
export TMPDIR="/tmp/lustre_shared/${USER}/${SLURM_JOBID}"

# We set application variables
export SCR=${TMPDIR}

# We set auxiliary variables
INPUT_DIR="input"
OUTPUT_DIR="output"
OUTPUT_FILE="OUTPUT"

# Create a temporary directory
mkdir -p ${TMPDIR}

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

# Go to the $TMPDIR directory
cd $TMPDIR

# We do the calculations
samtools view -b -S -o sim_reads_aligned.bam sim_reads_aligned.sam

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

End of calculations [$(date)].

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

# We finish the calculations, copy the contents of the $TMPDIR/output directory
# to the 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

Example input: Below are the files that should be in the input directory.
File:Samtools input.zip