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1 #/bin/bash
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2 #
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3 # This program is free software; you can redistribute it and/or modify
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4 # it under the terms of the GNU General Public License as published by
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5 # the Free Software Foundation; either version 3 of the License, or
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6 # (at your option) any later version.
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7 #
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8 # Copyright (C) 2009-2013 Max Planck Society, Sloan-Kettering Institute
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9 #
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10
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11 set -e
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12 echo "To get more information please run: configure -h"
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13 if [ $# != "0" ];
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14 then
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15 if [ "$1" == "-h" -o $# != "1" ];
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16 then
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17 echo Usage: $0 -h \(this help\)
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18 echo Usage: $0 -i \(interactive configuration\)
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19 echo Usage: $0 [-a] \(automatic configuration\)
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20 exit -1
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21 fi
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22 fi
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23
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24 . ./bin/rdiff_config.sh
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25
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26 echo ======================================
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27 echo rDiff configure \(version $RDIFF_VERSION\)
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28 echo ======================================
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29 echo
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30
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31 if [ "$1" == "-i" ];
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32 then
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33 echo rDiff base directory \(currently set to \"$RDIFF_PATH\", suggest to set to \"`pwd`\", used if left empty\)
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34 read RDIFF_PATH
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35 else
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36 echo "Running automatic configuration"
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37 RDIFF_PATH=""
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38 fi
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39 if [ "$RDIFF_PATH" == "" ];
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40 then
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41 RDIFF_PATH=`pwd`
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42 fi
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43 echo '=>' Setting rDiff base directory to \"$RDIFF_PATH\"
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44 echo
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45
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46 if [ "$1" == "-i" ];
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47 then
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48 echo SAMTools directory \(currently set to \"$RDIFF_SAMTOOLS_BIN_DIR\", system version used if left empty\)
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49 read RDIFF_SAMTOOLS_BIN_DIR
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50 else
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51 echo Checking for samtools
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52 RDIFF_SAMTOOLS_BIN_DIR=""
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53 fi
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54 if [ "$RDIFF_SAMTOOLS_BIN_DIR" == "" ];
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55 then
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56 if [ "$(which samtools)" != "" ] ;
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57 then
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58 RDIFF_SAMTOOLS_BIN_DIR=$(which samtools)
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59 if [ -f $(dirname $(which samtools))/../include/bam/sam.h ]
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60 then
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61 RDIFF_SAMTOOLS_INCLUDE_DIR=$(dirname $(which samtools))/../include/bam/
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62 echo "Include found: $RDIFF_SAMTOOLS_INCLUDE_DIR"
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63 elif [ -f $(dirname $(which samtools))/sam.h ]
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64 then
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65 RDIFF_SAMTOOLS_INCLUDE_DIR=$(dirname $(which samtools))/
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66 echo "Include found: $RDIFF_SAMTOOLS_INCLUDE_DIR"
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67 else
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68 echo "ERROR: Include sam.h include not found"
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69 exit -1 ;
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70 fi
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71 if [ -f $(dirname $(which samtools))/../lib/libbam.a ]
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72 then
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73 RDIFF_SAMTOOLS_LIB_DIR=$(dirname $(which samtools))/../lib/
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74 echo "Library found: $RDIFF_SAMTOOLS_LIB_DIR"
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75 elif [ -f $(dirname $(which samtools))/libbam.a ]
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76 then
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77 RDIFF_SAMTOOLS_LIB_DIR=$(dirname $(which samtools))/
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78 echo "Library found: $RDIFF_SAMTOOLS_LIB_DIR"
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79 else
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80 echo "ERROR: Library libbam.a not found"
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81 exit -1 ;
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82 fi
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83 else
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84 echo SAMTools libraries not found
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85 echo please run interactive mode: ./configure -i
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86 exit -1 ;
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87 fi
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88 else
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89 if [ ! -f $RDIFF_SAMTOOLS_BIN_DIR ];
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90 then
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91 echo "ERROR: Binary $RDIFF_SAMTOOLS_BIN_DIR not found"
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92 echo please run interactive mode: ./configure -i
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93 exit -1 ;
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94 fi
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95
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96 echo SAMTools Include directory \(currently set to \"$RDIFF_SAMTOOLS_INCLUDE_DIR\"\)
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97 read RDIFF_SAMTOOLS_INCLUDE_DIR
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98 if [ ! -f $RDIFF_SAMTOOLS_INCLUDE_DIR/sam.h ]
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99 then
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100 echo "ERROR: Include $RDIFF_SAMTOOLS_INCLUDE_DIR/sam.h include not found"
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101 echo please run interactive mode: ./configure -i
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102 exit -1 ;
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103 fi
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104
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105 echo SAMTools library directory \(currently set to \"$RDIFF_SAMTOOLS_LIB_DIR\"\)
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106 read RDIFF_SAMTOOLS_LIB_DIR
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107 if [ ! -f $RDIFF_SAMTOOLS_LIB_DIR/libbam.a ]
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108 then
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109 echo "ERROR: Library $RDIFF_SAMTOOLS_LIB_DIR/libbam.a include not found"
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110 echo please run interactive mode: ./configure -i
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111 exit -1 ;
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112 fi
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113 fi
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114 echo '=>' Setting samtools directory to \"$RDIFF_SAMTOOLS_BIN_DIR\"
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115 echo
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116
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117 if [ "$1" == "-i" ];
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118 then
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119 echo Path to the python binary \(currently set to \"$RDIFF_PYTHON_PATH\", system version used, if left empty\)
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120 read RDIFF_PYTHON_PATH
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121 else
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122 echo Checking for python and Scipy
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123 RDIFF_PYTHON_PATH=""
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124 fi
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125 if [ "$RDIFF_PYTHON_PATH" == "" ];
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126 then
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127 python_found=
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128 scipy_found=
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129 for i in python python2.7 python2.6 python2.5 python2.4;
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130 do
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131 RDIFF_PYTHON_PATH=`which $i`
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132 python_found=$i
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133 if [ "$RDIFF_PYTHON_PATH" != "" ];
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134 then
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135 scipy=`echo import scipy | $RDIFF_PYTHON_PATH 2>&1 | grep -e ImportError|wc -l`
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136 if [ $scipy == "0" ];
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137 then
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138 scipy_found=$RDIFF_PYTHON_PATH
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139 break
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140 fi
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141 fi
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142 done
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143 if [ "$python_found" == "" ];
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144 then
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145 echo "ERROR: Python not found"
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146 echo please run interactive mode: ./configure -i
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147 exit -1
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148 fi
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149 if [ "$scipy_found" == "" ];
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150 then
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151 echo "ERROR: Scipy not found (for $python_found)"
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152 echo please run interactive mode: ./configure -i
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153 exit -1
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154 fi
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155 fi
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156 echo '=>' Setting Python path to \"$RDIFF_PYTHON_PATH\"
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157 echo
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158
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159 RDIFF_INTERPRETER="octave"
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160 if [ "$RDIFF_INTERPRETER" == 'octave' ];
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161 then
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162 if [ "$1" == "-i" ];
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163 then
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164 echo Please enter the full path to octave \(currently set to \"$RDIFF_OCTAVE_BIN_PATH\", system version used, if left empty\)
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165 read RDIFF_OCTAVE_BIN_PATH
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166 else
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167 RDIFF_OCTAVE_BIN_PATH=""
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168 echo checking for octave
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169 fi
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170 if [ "$RDIFF_OCTAVE_BIN_PATH" == "" ];
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171 then
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172 RDIFF_OCTAVE_BIN_PATH=`which octave`
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173 if [ "$RDIFF_OCTAVE_BIN_PATH" == "" ];
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174 then
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175 echo octave not found
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176 echo please run interactive mode: ./configure -i
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177 exit -1
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178 fi
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179 fi
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180 echo '=>' Setting octave\'s path to \"$RDIFF_OCTAVE_BIN_PATH\"
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181 if [ "$1" == "-i" ];
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182 then
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183 echo Please enter the full path to mkoctfile \(currently set to \"$RDIFF_OCTAVE_MKOCT\", system version used, if left empty\)
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184 read RDIFF_OCTAVE_MKOCT
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185 else
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186 RDIFF_OCTAVE_MKOCT=""
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187 fi
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188 if [ "$RDIFF_OCTAVE_MKOCT" == "" ];
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189 then
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190 RDIFF_OCTAVE_MKOCT=`which mkoctfile`
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191 if [ "$RDIFF_OCTAVE_MKOCT" == "" ];
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192 then
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193 RDIFF_OCTAVE_MKOCT=$(dirname $RDIFF_OCTAVE_BIN_PATH)/mkoctfile
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194 if [ ! -f RDIFF_OCTAVE_MKOCT ];
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195 then
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196 echo mkoctfile not found
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197 echo please run interactive mode: ./configure -i
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198 exit -1
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199 fi
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200 fi
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201 fi
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202 echo '=>' Setting octave\'s path to \"$RDIFF_OCTAVE_MKOCT\"
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203 echo
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204 fi
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205
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206 if [ "$RDIFF_INTERPRETER" == 'matlab' ];
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207 then
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208 echo Please enter the full path to matlab \(currently set to \"$MATLAB_BIN_PATH\", system version used, if left empty\)
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209 read MATLAB_BIN_PATH
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210 if [ "$MATLAB_BIN_PATH" == "" ];
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211 then
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212 MATLAB_BIN_PATH=`which matlab`
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213 if [ "$MATLAB_BIN_PATH" == "" ];
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214 then
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215 echo matlab not found
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216 echo please run interactive mode: ./configure -i
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217 exit -1
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218 fi
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219 fi
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220 if [ ! -f $MATLAB_BIN_PATH ];
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221 then
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222 echo matlab not found
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223 echo please run interactive mode: ./configure -i
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224 exit -1
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225 fi
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226 echo '=>' Setting matlab\'s path to \"$MATLAB_BIN_PATH\"
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227 echo
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228
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229 echo Please enter the full path to mex binary \(currently set to \"$MATLAB_MEX_PATH\", system version used if left empty\)
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230 read MATLAB_MEX_PATH
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231 if [ "$MATLAB_MEX_PATH" == "" ];
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232 then
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233 MATLAB_MEX_PATH=`which mex`
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234 if [ "$MATLAB_MEX_PATH" == "" ];
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235 then
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236 echo mex not found
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237 echo please run interactive mode: ./configure -i
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238 exit -1
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239 fi
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240 fi
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241 if [ ! -f "$MATLAB_MEX_PATH" ];
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242 then
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243 echo mex not found
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244 echo please run interactive mode: ./configure -i
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245 exit -1
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246 fi
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247 echo '=>' Setting mex\' path to \"$MATLAB_MEX_PATH\"
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248 echo
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249
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250 echo Please enter the full path to the matlab include directory \(currently set to \"$MATLAB_INCLUDE_DIR\", system version used, if left empty\)
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251 read MATLAB_INCLUDE_DIR
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252 if [ "$MATLAB_INCLUDE_DIR" == "" ];
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253 then
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254 MATLAB_INCLUDE_DIR=$(dirname $MATLAB_BIN_PATH)/../extern/include
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255 fi
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256 if [ ! -d "$MATLAB_INCLUDE_DIR" ];
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257 then
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258 echo matlab include dir not found
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259 echo please run interactive mode: ./configure -i
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260 exit -1
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261 fi
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262 echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
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263 echo
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264
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265 RDIFF_OCTAVE_BIN_PATH=
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266 fi
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267
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268 cp -p bin/rdiff_config.sh bin/rdiff_config.sh.bak
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269
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270 grep -v -e RDIFF_OCTAVE_BIN_PATH -e RDIFF_OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
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271 -e RDIFF_PATH -e RDIFF_SRC_PATH -e RDIFF_BIN_PATH \
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272 -e RDIFF_INTERPRETER bin/rdiff_config.sh.bak \
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273 -e RDIFF_SAMTOOLS_BIN_DIR -e RDIFF_SAMTOOLS_LIB_DIR -e RDIFF_SAMTOOLS_INCLUDE_DIR -e RDIFF_PYTHON_PATH -e SCIPY_PATH -e $RDIFF_VERSION > bin/rdiff_config.sh
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274
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275 echo Generating config file ...
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276
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277 # appending the relevant lines to rdiff_config.sh
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278 echo export RDIFF_VERSION=$RDIFF_VERSION >> bin/rdiff_config.sh
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279 echo export RDIFF_PATH=$RDIFF_PATH >> bin/rdiff_config.sh
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280 echo export RDIFF_SRC_PATH=${RDIFF_PATH}/src >> bin/rdiff_config.sh
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281 echo export RDIFF_BIN_PATH=${RDIFF_PATH}/bin >> bin/rdiff_config.sh
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282 echo export RDIFF_INTERPRETER=$RDIFF_INTERPRETER >> bin/rdiff_config.sh
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283 echo export RDIFF_MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/rdiff_config.sh
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284 echo export RDIFF_MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/rdiff_config.sh
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285 echo export RDIFF_MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/rdiff_config.sh
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286 echo export RDIFF_OCTAVE_BIN_PATH=$RDIFF_OCTAVE_BIN_PATH >> bin/rdiff_config.sh
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287 echo export RDIFF_OCTAVE_MKOCT=$RDIFF_OCTAVE_MKOCT >> bin/rdiff_config.sh
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288 echo export RDIFF_SAMTOOLS_BIN_DIR=$RDIFF_SAMTOOLS_BIN_DIR >> bin/rdiff_config.sh
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289 echo export RDIFF_SAMTOOLS_LIB_DIR=$RDIFF_SAMTOOLS_LIB_DIR >> bin/rdiff_config.sh
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290 echo export RDIFF_SAMTOOLS_INCLUDE_DIR=$RDIFF_SAMTOOLS_INCLUDE_DIR >> bin/rdiff_config.sh
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291 echo export RDIFF_PYTHON_PATH=$RDIFF_PYTHON_PATH >> bin/rdiff_config.sh
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292
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293 echo Done.
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294 echo
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295
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296 echo Please use \'make\' to compile the mex files before using rDiff.
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297 echo To test rDiff use \'make example\' or \'make threeexamples\'.
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298 echo
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