run_dREG-HD.bsh

#!/bin/bash

if [ "$#" -lt 5 ]; then
	echo ""
	echo "USAGE: bash run_dREG-HD.bsh dREG_bed plus_strand.bw minus_strand.bw HD_model.rdata [nthreads] [GPU]"
	echo ""
	echo "dREG_bed -- the dREG peaks in bed format."
	echo "plus_strand.bw	-- PRO-seq data (plus  strand) formatted as a bigWig file."
	echo "minus_strand.bw	-- PRO-seq data (minus strand) formatted as a bigWig file."
	echo "HD_model.rdata	-- The path to the RData file containing the pre-trained dREG-HD SVM model."
	echo "[nthreads]	-- [optional, default=1] The number of threads to use when evaluating dREG-HD sites."
	echo "[GPU]	        -- [optional, gpu or blank, default is blank] indicating whether GPU package can be used."
	echo ""
	exit 1
fi

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

bed=$1
bwPL=$2
bwMN=$3
model=$4
gpu=FALSE
ncores=1

if [ "$#" -gt 4 ]; then
	ncores=$5
else
	ncores=1
fi

if [ "$#" -gt 5 ]; then
	gpu=$6
fi


echo "Using: R --vanilla --slave --args $bed $bwPL $bwMN $model $ncores $gpu < $bsh_path/run_dREG-HD.R"
R --vanilla --slave --args $bed $bwPL $bwMN $model $ncores $gpu < $bsh_path/run_dREG-HD.R