run_dTOX.bsh

#!/usr/bin/bash

if [ "$#" -lt 5 ]; then
    echo ""
    echo "USAGE: bash run_dTOX.bsh plus_strand_bw minus_strand_bw seq.type hg19 out_prefix gpu_cores cpu_cores"
    echo ""
    echo "genome_id       -- Currently hg19 and mm10 are available by default."
    echo "Sequeue Type    -- ATAC-seq, DNASE-1-seq or PRO-seq "
    echo "plus_strand.bw  -- Seqence data (plus strand).  Read counts (not normalized) formatted as a bigWig file. "
    echo "minus_strand.bw -- Seqence data (minus strand). Read counts (not normalized) formatted as a bigWig file. "
    echo "out_prefix      -- The prefix of the output file. "
    echo "gpu_cores       -- [optional, default=1] indicating how many GPU cores can be used"    
    echo "cpu_cores       -- [optional, default=16] indicating how many CPU cores can be used. "

    exit 1
fi

pushd `dirname $0` > /dev/null
bsh_path=`pwd`
popd > /dev/null

genome_id=$1
seq_type=$2
bwPlus=$3
bwMinus=$4
out_prefix=$5
using_filter=$6

gpu_cores=1
if [ "$#" -gt 6 ]; then
#	[[ $6 !~ ^?[0-9]+$ ]]
	gpu_cores=$7
fi

cpu_cores=16
if [ "$#" -gt 7 ]; then
	cpu_cores=$8
fi

out_file=${out_prefix}.dTOX.bound.bed.gz

echo "Using: R --vanilla --slave --args $genome_id $seq_type $bwPlus $bwMinus  $out_file $bsh_path $using_filter $gpu_cores $cpu_cores < $bsh_path/Rscript/run-dTOX.R > run-dTOX.log"
R --vanilla --slave --args $genome_id $seq_type $bwPlus $bwMinus $out_file $bsh_path $using_filter $gpu_cores $cpu_cores < $bsh_path/Rscript/run-dTOX.R > run-dTOX.log