--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/setup_deseq-hts.sh	Wed May 09 20:43:47 2012 -0400
@@ -0,0 +1,192 @@
+#!/bin/bash
+set -e 
+
+. ./bin/deseq_config.sh
+
+echo ==========================================
+echo  DESeq-hts setup script \(DESeq version $DESEQ_VERSION\) 
+echo ==========================================
+echo
+echo DESeq-hts base directory \(currently set to \"$DESEQ_PATH\", suggest to set to \"`pwd`\", used if left empty\)
+read DESEQ_PATH
+if [ "$DESEQ_PATH" == "" ];
+then
+	DESEQ_PATH=`pwd`
+fi
+echo '=>' Setting DESeq-hts base directory to \"$DESEQ_PATH\"
+echo
+
+echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\)
+read SAMTOOLS_DIR
+if [ "$SAMTOOLS_DIR" == "" ];
+then
+	if [ "$(which samtools)" != "" ] ;
+	then
+		SAMTOOLS_DIR=$(dirname $(which samtools)) 
+	else
+		echo samtools not found
+		exit -1 ;
+	fi
+fi
+echo '=>' Setting SAMTools directory to \"$SAMTOOLS_DIR\"
+echo
+
+echo Path to the python binary \(currently set to \"$PYTHON_PATH\", system version used, if left empty\)
+read PYTHON_PATH
+if [ "$PYTHON_PATH" == "" ];
+then
+    PYTHON_PATH=`which python`
+	if [ "$PYTHON_PATH" == "" ];
+	then
+		echo python not found
+		exit -1 
+	fi
+fi
+echo '=>' Setting Python path to \"$PYTHON_PATH\"
+echo
+
+echo Path to the R binary \(currently set to \"$R_PATH\", system version used, if left empty\)
+read R_PATH
+if [ "$R_PATH" == "" ];
+then
+    R_PATH=`which R`
+	if [ "$R_PATH" == "" ];
+	then
+		echo R not found
+		exit -1 
+	fi
+fi
+echo '=>' Setting R path to \"$R_PATH\"
+echo
+
+echo Path to Scipy library files \(currently set to \"$SCIPY_PATH\", system version is used if left empty\)
+read SCIPY_PATH
+echo '=>' Setting Scipy path to \"$SCIPY_PATH\"
+echo
+
+echo Which interpreter should be used \(\"octave\" or \"matlab\"\)
+read INTERPRETER  
+if [ "$INTERPRETER" != 'octave' -a  "$INTERPRETER" != 'matlab' ];
+then
+	echo Unrecognized choice: \"$INTERPRETER\"
+	echo Aborting
+	false
+fi
+echo '=>' Setting interpreter to \"$INTERPRETER\"
+echo
+
+if [ "$INTERPRETER" == 'octave' ];
+then
+	echo Please enter the full path to octave \(currently set to \"$OCTAVE_BIN_PATH\", system version used, if left empty\)
+	read OCTAVE_BIN_PATH
+	if [ "$OCTAVE_BIN_PATH" == "" ];
+	then
+	    OCTAVE_BIN_PATH=`which octave` 
+		if [ "$OCTAVE_BIN_PATH" == "" ];
+		then
+			echo octave not found
+			exit -1
+		fi
+	fi
+	echo '=>' Setting octave\'s path to \"$OCTAVE_BIN_PATH\"
+	echo
+	echo Please enter the full path to mkoctfile \(currently set to \"$OCTAVE_MKOCT\", system version used, if left empty\)
+	read OCTAVE_MKOCT
+	if [ "$OCTAVE_MKOCT" == "" ];
+	then
+	    OCTAVE_MKOCT=`which mkoctfile` 
+		if [ "$OCTAVE_MKOCT" == "" ];
+		then
+			OCTAVE_MKOCT=$(dirname $OCTAVE_BIN_PATH)/mkoctfile
+			if [ ! -f OCTAVE_MKOCT ];
+			then
+				echo mkoctfile not found
+				exit -1
+			fi
+		fi
+	fi
+	echo '=>' Setting mkoctfile\'s path to \"$OCTAVE_MKOCT\"
+	echo
+	MATLAB_BIN_PATH=
+fi
+if [ "$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
+			exit -1
+		fi
+	fi
+	if [ ! -f $MATLAB_BIN_PATH ];
+	then
+		echo matlab not found
+		exit -1
+	fi
+	echo '=>' Setting matlab\'s path to \"$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
+			exit -1
+		fi
+	fi
+	if [ ! -f "$MATLAB_MEX_PATH" ];
+	then
+		echo mex not found
+		exit -1
+	fi
+	echo '=>' Setting mex\' path to \"$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
+		exit -1
+	fi
+	echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
+	echo
+	OCTAVE_BIN_PATH=
+fi
+
+cp -p bin/deseq_config.sh bin/deseq_config.sh.bk
+grep -v -e OCTAVE_BIN_PATH -e OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
+    -e DESEQ_PATH -e DESEQ_SRC_PATH -e DESEQ_BIN_PATH \
+    -e INTERPRETER -e SAMTOOLS_DIR -e PYTHON_PATH -e SCIPY_PATH -e R_PATH -e $DESEQ_VERSION bin/deseq_config.sh.bk  \
+    > bin/deseq_config.sh
+echo
+echo
+echo generating config file
+
+echo export DESEQ_VERSION=$DESEQ_VERSION >> bin/deseq_config.sh
+echo export DESEQ_PATH=$DESEQ_PATH >> bin/deseq_config.sh
+echo export DESEQ_SRC_PATH=${DESEQ_PATH}/src >> bin/deseq_config.sh
+echo export DESEQ_BIN_PATH=${DESEQ_PATH}/bin >> bin/deseq_config.sh
+echo export INTERPRETER=$INTERPRETER >> bin/deseq_config.sh
+echo export MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/deseq_config.sh
+echo export MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/deseq_config.sh
+echo export MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/deseq_config.sh
+echo export OCTAVE_BIN_PATH=$OCTAVE_BIN_PATH >> bin/deseq_config.sh
+echo export OCTAVE_MKOCT=$OCTAVE_MKOCT >> bin/deseq_config.sh
+echo export SAMTOOLS_DIR=$SAMTOOLS_DIR >> bin/deseq_config.sh
+echo export PYTHON_PATH=$PYTHON_PATH >> bin/deseq_config.sh
+echo export SCIPY_PATH=$SCIPY_PATH >> bin/deseq_config.sh
+echo export R_PATH=$R_PATH >> bin/deseq_config.sh
+
+echo
+echo Done.
+echo