Bedtools

Program description:
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyzes can be conducted by combining multiple bedtools operations on the UNIX command line.

Versions:

Name: bedtools
Version: 2.21.0
Platform: x86_64
Category: Applications/Engineering
URL http://bedtools.readthedocs.org/en/latest/index.html
Provides: bedtools

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 bedtools
module load gcc

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

# 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
bedtools intersect -a cpg.bed -b exons.bed | head -5 > result.txt

# 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

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