scripts for running RACS scaling analysis

diff --git a/tools/ScalingAnalysis/ORF_RACS-template.sh b/tools/ScalingAnalysis/ORF_RACS-template.sh
new file mode 100755
index 0000000..959e03a
--- /dev/null
+++ b/tools/ScalingAnalysis/ORF_RACS-template.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+#
+# Shell script template that can be used for running the ORF-RACS pipeline in a
+# set of different experiments.
+#
+# This script will run the RACS scripts in background, which is achieved by
+# including the "&" symbol at the end of each call to the RACS script.
+
+cores=${1:-"1"}
+
+# define location of the RACS pipeline and script to run, in this case "countReads.sh"
+RACSscript="$HOME/RESEARCH/racs/core/countReads.sh"
+
+# define location of data and reference files
+dataDIR="$SCRATCH/TT/DATA/data1_BD1-2"
+refsDIR="$SCRATCH/GPC/scratch2/Tetrahymena_Ryerson/REFS"
+
+# specify reference and annotation files
+refsFILE="T_thermophila_June2014.gff3"
+fastaFILE="T_thermophila_June2014_assembly.fasta"
+
+workingDIR="/dev/shm"
+
+# start tracer...
+. $HOME/RESEARCH/STATS/tracer.sh "du -s $workingDIR/$USER" &
+trPID=$!
+
+# run pipeline
+$RACSscript	\
+	$dataDIR/BD1_INPUT.fastq.gz	\
+	$dataDIR/BD1_IP.fastq.gz	\
+	$refsDIR/$fastaFILE  $refsDIR/$refsFILE	\
+	$workingDIR	\
+	$cores
+
+#wait
+
+# terminate tracer...
+kill -9 $trPID
+#pkill watch
diff --git a/tools/ScalingAnalysis/ScalingAnalysis.sh b/tools/ScalingAnalysis/ScalingAnalysis.sh
new file mode 100755
index 0000000..eecc5fb
--- /dev/null
+++ b/tools/ScalingAnalysis/ScalingAnalysis.sh
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+#!/bin/bash
+
+# reverse order -- to run first tests faster
+#cores="32 16 8 4 2  1"
+cores="1 2 4 8 16 32 64"
+
+for i in $cores; do
+	dir=${i}"cores";
+	echo $i ... $dir;
+	mkdir $dir; cd $dir;
+	echo "processing... `pwd`";
+	. ../ORF_RACS-template.sh $i ;  #>  /dev/null 2>&1 ;
+	cd ..;
+done
+
+./checkResults.sh
diff --git a/tools/ScalingAnalysis/checkResults.sh b/tools/ScalingAnalysis/checkResults.sh
new file mode 100755
index 0000000..d5b40f7
--- /dev/null
+++ b/tools/ScalingAnalysis/checkResults.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# script for testing results from scaling analysis
+# sanity check for results!
+
+files=`ls -1 *cores/ORF*/FINAL*`
+
+for i in $files; do
+	target=`basename $i`
+done
+
+dirs=`ls -d *cores/ORF*`
+
+nbrTests=0
+nbrFailedTests=0
+nbrPassedTests=0
+
+for i in $dirs; do
+	for j in $dirs; do
+		nbrTests=$((nbrTests+1));
+		echo "comparing $i/$target vs $j/$target";
+		comparison=$( diff $i/$target $j/$target );
+		exit_code=$?;  #echo ${exit_code};
+		if [[ $exit_code -eq "0" ]]; then
+			echo -e "\t >>> test succesful... "
+			nbrPassedTests=$((nbrPassedTests+1))
+		else
+			echo "***** ERROR !!! when checking results failed at $i/$target VS $j/$target"
+			nbrFailedTests=$((nbrFailedTests+1))
+		fi
+	done;
+done
+
+echo $target
+
+echo "Number of Tests Passed: $nbrPassedTests"
+echo "Number of Checks Failed: $nbrFailedTests"
+echo "Total Number of files compared: $nbrTests"