--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/configure	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,298 @@
+#/bin/bash
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# Copyright (C) 2009-2013 Max Planck Society, Sloan-Kettering Institute
+#
+
+set -e 
+echo "To get more information please run: configure -h" 
+if [ $# != "0" ];
+then
+		if [ "$1" == "-h" -o $# != "1" ];
+        then
+		  echo Usage: $0 -h   \(this help\)
+		  echo Usage: $0 -i   \(interactive configuration\)
+		  echo Usage: $0 [-a] \(automatic configuration\)
+  		  exit -1
+        fi
+fi
+
+. ./bin/rdiff_config.sh
+
+echo ======================================
+echo  rDiff configure \(version $RDIFF_VERSION\) 
+echo ======================================
+echo
+
+if [ "$1" == "-i" ];
+then
+  echo rDiff base directory \(currently set to \"$RDIFF_PATH\", suggest to set to \"`pwd`\", used if left empty\)
+  read RDIFF_PATH       
+else
+  echo "Running automatic configuration"
+  RDIFF_PATH=""
+fi
+if [ "$RDIFF_PATH" == "" ];
+then
+	RDIFF_PATH=`pwd`
+fi
+echo '=>' Setting rDiff base directory to \"$RDIFF_PATH\"
+echo
+
+if [ "$1" == "-i" ];
+then
+  echo SAMTools directory \(currently set to \"$RDIFF_SAMTOOLS_BIN_DIR\", system version used if left empty\)
+  read RDIFF_SAMTOOLS_BIN_DIR
+else   
+  echo Checking for samtools
+  RDIFF_SAMTOOLS_BIN_DIR=""
+fi
+if [ "$RDIFF_SAMTOOLS_BIN_DIR" == "" ];
+then
+	if [ "$(which samtools)" != "" ] ;
+	then
+		RDIFF_SAMTOOLS_BIN_DIR=$(which samtools)
+	    if [ -f $(dirname $(which samtools))/../include/bam/sam.h ]
+	    then
+			RDIFF_SAMTOOLS_INCLUDE_DIR=$(dirname $(which samtools))/../include/bam/
+			echo "Include found: $RDIFF_SAMTOOLS_INCLUDE_DIR"
+	    elif [ -f $(dirname $(which samtools))/sam.h ]
+	    then 
+	               RDIFF_SAMTOOLS_INCLUDE_DIR=$(dirname $(which samtools))/
+                       echo "Include found: $RDIFF_SAMTOOLS_INCLUDE_DIR"
+	    else
+			echo "ERROR: Include sam.h include not found"
+			exit -1 ;
+	    fi
+	    if [ -f $(dirname $(which samtools))/../lib/libbam.a ]
+	    then
+			RDIFF_SAMTOOLS_LIB_DIR=$(dirname $(which samtools))/../lib/
+			echo "Library found: $RDIFF_SAMTOOLS_LIB_DIR"
+	    elif [ -f $(dirname $(which samtools))/libbam.a ]
+	    then
+		       RDIFF_SAMTOOLS_LIB_DIR=$(dirname $(which samtools))/
+                       echo "Library found: $RDIFF_SAMTOOLS_LIB_DIR"
+	    else
+			echo "ERROR: Library libbam.a not found"
+			exit -1 ;
+	    fi
+	else
+	    echo SAMTools libraries not found
+	    echo please run interactive mode: ./configure -i
+	    exit -1 ;
+	fi
+else
+	if [ ! -f $RDIFF_SAMTOOLS_BIN_DIR ];
+	then
+		echo "ERROR: Binary $RDIFF_SAMTOOLS_BIN_DIR not found"
+                echo please run interactive mode: ./configure -i
+		exit -1 ;
+	fi
+
+	echo SAMTools Include directory \(currently set to \"$RDIFF_SAMTOOLS_INCLUDE_DIR\"\)
+	read RDIFF_SAMTOOLS_INCLUDE_DIR
+	if [ ! -f $RDIFF_SAMTOOLS_INCLUDE_DIR/sam.h ]
+	then
+		echo "ERROR: Include $RDIFF_SAMTOOLS_INCLUDE_DIR/sam.h include not found"
+                echo please run interactive mode: ./configure -i
+		exit -1 ;
+	fi
+	
+	echo SAMTools library directory \(currently set to \"$RDIFF_SAMTOOLS_LIB_DIR\"\)
+	read RDIFF_SAMTOOLS_LIB_DIR
+	if [ ! -f $RDIFF_SAMTOOLS_LIB_DIR/libbam.a ]
+	then
+		echo "ERROR: Library $RDIFF_SAMTOOLS_LIB_DIR/libbam.a include not found"
+                echo please run interactive mode: ./configure -i
+		exit -1 ;
+	fi
+fi
+echo '=>' Setting samtools directory to \"$RDIFF_SAMTOOLS_BIN_DIR\"
+echo
+
+if [ "$1" == "-i" ];
+then
+  echo Path to the python binary \(currently set to \"$RDIFF_PYTHON_PATH\", system version used, if left empty\)
+  read RDIFF_PYTHON_PATH
+else
+  echo Checking for python and Scipy
+  RDIFF_PYTHON_PATH="" 
+fi
+if [ "$RDIFF_PYTHON_PATH" == "" ];
+then
+	python_found=
+    scipy_found=
+	for i in python python2.7 python2.6 python2.5 python2.4;
+    do	
+      RDIFF_PYTHON_PATH=`which $i`
+  	  python_found=$i
+  	  if [ "$RDIFF_PYTHON_PATH" != "" ];
+ 	  then
+	    scipy=`echo import scipy | $RDIFF_PYTHON_PATH 2>&1 | grep  -e ImportError|wc -l`
+		if [ $scipy == "0" ];
+        then
+		  scipy_found=$RDIFF_PYTHON_PATH
+          break
+		fi
+	  fi
+    done 
+    if [ "$python_found" == "" ];
+    then 
+      echo "ERROR: Python not found"
+      echo please run interactive mode: ./configure -i
+      exit -1 
+    fi
+    if [ "$scipy_found" == "" ];
+    then 
+      echo "ERROR: Scipy not found (for $python_found)"
+      echo please run interactive mode: ./configure -i
+      exit -1 
+    fi
+fi
+echo '=>' Setting Python path to \"$RDIFF_PYTHON_PATH\"
+echo
+
+RDIFF_INTERPRETER="octave"
+if [ "$RDIFF_INTERPRETER" == 'octave' ];
+then
+  if [ "$1" == "-i" ];
+  then
+	echo Please enter the full path to octave \(currently set to \"$RDIFF_OCTAVE_BIN_PATH\", system version used, if left empty\)
+	read RDIFF_OCTAVE_BIN_PATH
+  else
+    RDIFF_OCTAVE_BIN_PATH="" 
+	echo checking for octave 
+  fi
+	if [ "$RDIFF_OCTAVE_BIN_PATH" == "" ];
+	then
+	    RDIFF_OCTAVE_BIN_PATH=`which octave` 
+		if [ "$RDIFF_OCTAVE_BIN_PATH" == "" ];
+		then
+			echo octave not found
+                        echo please run interactive mode: ./configure -i
+			exit -1
+		fi
+	fi
+	echo '=>' Setting octave\'s path to \"$RDIFF_OCTAVE_BIN_PATH\"
+  if [ "$1" == "-i" ];
+  then
+	echo Please enter the full path to mkoctfile \(currently set to \"$RDIFF_OCTAVE_MKOCT\", system version used, if left empty\)
+	read RDIFF_OCTAVE_MKOCT
+  else 
+    RDIFF_OCTAVE_MKOCT="" 
+  fi
+	if [ "$RDIFF_OCTAVE_MKOCT" == "" ];
+	then
+	    RDIFF_OCTAVE_MKOCT=`which mkoctfile` 
+		if [ "$RDIFF_OCTAVE_MKOCT" == "" ];
+		then
+			RDIFF_OCTAVE_MKOCT=$(dirname $RDIFF_OCTAVE_BIN_PATH)/mkoctfile
+			if [ ! -f RDIFF_OCTAVE_MKOCT ];
+			then
+				echo mkoctfile not found
+				echo please run interactive mode: ./configure -i
+				exit -1
+			fi
+		fi
+	fi
+	echo '=>' Setting octave\'s path to \"$RDIFF_OCTAVE_MKOCT\"
+	echo
+fi
+
+if [ "$RDIFF_INTERPRETER" == 'matlab' ];
+then
+	echo Please enter the full path to matlab \(currently set to \"$MATLAB_BIN_PATH\", system version used, if left empty\)
+	read MATLAB_BIN_PATH
+	if [ "$MATLAB_BIN_PATH" == "" ];
+	then
+		MATLAB_BIN_PATH=`which matlab`
+		if [ "$MATLAB_BIN_PATH" == "" ];
+		then
+			echo matlab not found
+			echo please run interactive mode: ./configure -i
+			exit -1
+		fi
+	fi
+	if [ ! -f $MATLAB_BIN_PATH ];
+	then
+		echo matlab not found
+		echo please run interactive mode: ./configure -i
+		exit -1
+	fi
+	echo '=>' Setting matlab\'s path to \"$MATLAB_BIN_PATH\"
+	echo
+
+	echo Please enter the full path to mex binary \(currently set to \"$MATLAB_MEX_PATH\", system version used if left empty\)
+	read MATLAB_MEX_PATH
+	if [ "$MATLAB_MEX_PATH" == "" ];
+	then
+		MATLAB_MEX_PATH=`which mex`
+		if [ "$MATLAB_MEX_PATH" == "" ];
+		then
+			echo mex not found
+			echo please run interactive mode: ./configure -i
+			exit -1
+		fi
+	fi
+	if [ ! -f "$MATLAB_MEX_PATH" ];
+	then
+		echo mex not found
+		echo please run interactive mode: ./configure -i
+		exit -1
+	fi
+	echo '=>' Setting mex\' path to \"$MATLAB_MEX_PATH\"
+	echo
+
+	echo Please enter the full path to the matlab include directory \(currently set to \"$MATLAB_INCLUDE_DIR\", system version used, if left empty\)
+	read MATLAB_INCLUDE_DIR
+	if [ "$MATLAB_INCLUDE_DIR" == "" ];
+	then
+		MATLAB_INCLUDE_DIR=$(dirname $MATLAB_BIN_PATH)/../extern/include
+	fi
+	if [ ! -d "$MATLAB_INCLUDE_DIR" ];
+	then
+		echo matlab include dir not found
+		echo please run interactive mode: ./configure -i
+		exit -1
+	fi
+	echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
+	echo
+
+	RDIFF_OCTAVE_BIN_PATH=
+fi
+
+cp -p bin/rdiff_config.sh bin/rdiff_config.sh.bak
+
+grep -v -e RDIFF_OCTAVE_BIN_PATH -e RDIFF_OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
+    -e RDIFF_PATH -e RDIFF_SRC_PATH -e RDIFF_BIN_PATH \
+    -e RDIFF_INTERPRETER bin/rdiff_config.sh.bak \
+    -e RDIFF_SAMTOOLS_BIN_DIR -e RDIFF_SAMTOOLS_LIB_DIR -e RDIFF_SAMTOOLS_INCLUDE_DIR -e RDIFF_PYTHON_PATH -e SCIPY_PATH -e $RDIFF_VERSION > bin/rdiff_config.sh
+
+echo Generating config file ... 
+
+# appending the relevant lines to rdiff_config.sh
+echo export RDIFF_VERSION=$RDIFF_VERSION >> bin/rdiff_config.sh
+echo export RDIFF_PATH=$RDIFF_PATH >> bin/rdiff_config.sh
+echo export RDIFF_SRC_PATH=${RDIFF_PATH}/src >> bin/rdiff_config.sh
+echo export RDIFF_BIN_PATH=${RDIFF_PATH}/bin >> bin/rdiff_config.sh
+echo export RDIFF_INTERPRETER=$RDIFF_INTERPRETER >> bin/rdiff_config.sh
+echo export RDIFF_MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/rdiff_config.sh
+echo export RDIFF_MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/rdiff_config.sh
+echo export RDIFF_MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/rdiff_config.sh
+echo export RDIFF_OCTAVE_BIN_PATH=$RDIFF_OCTAVE_BIN_PATH >> bin/rdiff_config.sh
+echo export RDIFF_OCTAVE_MKOCT=$RDIFF_OCTAVE_MKOCT >> bin/rdiff_config.sh
+echo export RDIFF_SAMTOOLS_BIN_DIR=$RDIFF_SAMTOOLS_BIN_DIR >> bin/rdiff_config.sh  
+echo export RDIFF_SAMTOOLS_LIB_DIR=$RDIFF_SAMTOOLS_LIB_DIR >> bin/rdiff_config.sh  
+echo export RDIFF_SAMTOOLS_INCLUDE_DIR=$RDIFF_SAMTOOLS_INCLUDE_DIR >> bin/rdiff_config.sh  
+echo export RDIFF_PYTHON_PATH=$RDIFF_PYTHON_PATH >> bin/rdiff_config.sh
+
+echo Done.
+echo 
+
+echo Please use \'make\' to compile the mex files before using rDiff.
+echo To test rDiff use \'make example\' or \'make threeexamples\'.
+echo