standard.sh

#! /bin/bash

type mpiBWA

if [[ ! $? -eq 0 ]]
then
    echo "ERROR: mpiBWA not found in your PATH"
    exit 1
fi

output_dir=${HOME}/mpiBWAExample

if [[ ! -d ${output_dir} ]]
then
    mkdir -p ${output_dir}
    echo "INFO: the directory ${output_dir} has been created to store the results generated by mpiBWAExample"
fi

if [[ ! -f  ${output_dir}/hg19.small.fa ]]
then
    echo "INFO: untar the (small) reference human genome with bwa index"
    tar zxvf data/hg19.small.tar.gz --directory ${output_dir}
fi

if [[ ! -f ${output_dir}/hg19.small.fa.map ]]
then
    echo "INFO: creating the binary image of the (small) reference genome with mpiBWAIdx"
    mpiBWAIdx  ${output_dir}/hg19.small.fa
fi

echo "INFO: aligning the reads with mpiBWA"

mpirun -n 2 mpiBWA mem -t 8 -o ${output_dir}/HCC1187C.sam ${output_dir}/hg19.small.fa data/HCC1187C_R1_10K.fastq data/HCC1187C_R2_10K.fastq 2> ${output_dir}/mpiBWA.log

echo "INFO: mpiBWA.log is available in ${output_dir}"