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1 #!/bin/bash
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2 set -e
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3
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4 . ./bin/deseq_config.sh
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5
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6 echo ==========================================
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7 echo DESeq-hts setup script \(DESeq version $DESEQ_VERSION\)
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8 echo ==========================================
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9 echo
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10 echo DESeq-hts base directory \(currently set to \"$DESEQ_PATH\", suggest to set to \"`pwd`\", used if left empty\)
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11 read DESEQ_PATH
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12 if [ "$DESEQ_PATH" == "" ];
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13 then
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14 DESEQ_PATH=`pwd`
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15 fi
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16 echo '=>' Setting DESeq-hts base directory to \"$DESEQ_PATH\"
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17 echo
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18
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19 echo SAMTools directory \(currently set to \"$SAMTOOLS_DIR\", system version used if left empty\)
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20 read SAMTOOLS_DIR
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21 if [ "$SAMTOOLS_DIR" == "" ];
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22 then
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23 if [ "$(which samtools)" != "" ] ;
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24 then
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25 SAMTOOLS_DIR=$(dirname $(which samtools))
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26 else
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27 echo samtools not found
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28 exit -1 ;
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29 fi
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30 fi
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31 echo '=>' Setting SAMTools directory to \"$SAMTOOLS_DIR\"
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32 echo
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33
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34 echo Path to the python binary \(currently set to \"$PYTHON_PATH\", system version used, if left empty\)
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35 read PYTHON_PATH
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36 if [ "$PYTHON_PATH" == "" ];
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37 then
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38 PYTHON_PATH=`which python`
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39 if [ "$PYTHON_PATH" == "" ];
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40 then
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41 echo python not found
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42 exit -1
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43 fi
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44 fi
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45 echo '=>' Setting Python path to \"$PYTHON_PATH\"
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46 echo
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47
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48 echo Path to the R binary \(currently set to \"$R_PATH\", system version used, if left empty\)
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49 read R_PATH
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50 if [ "$R_PATH" == "" ];
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51 then
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52 R_PATH=`which R`
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53 if [ "$R_PATH" == "" ];
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54 then
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55 echo R not found
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56 exit -1
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57 fi
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58 fi
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59 echo '=>' Setting R path to \"$R_PATH\"
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60 echo
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61
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62 echo Path to Scipy library files \(currently set to \"$SCIPY_PATH\", system version is used if left empty\)
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63 read SCIPY_PATH
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64 echo '=>' Setting Scipy path to \"$SCIPY_PATH\"
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65 echo
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66
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67 echo Which interpreter should be used \(\"octave\" or \"matlab\"\)
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68 read INTERPRETER
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69 if [ "$INTERPRETER" != 'octave' -a "$INTERPRETER" != 'matlab' ];
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70 then
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71 echo Unrecognized choice: \"$INTERPRETER\"
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72 echo Aborting
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73 false
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74 fi
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75 echo '=>' Setting interpreter to \"$INTERPRETER\"
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76 echo
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77
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78 if [ "$INTERPRETER" == 'octave' ];
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79 then
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80 echo Please enter the full path to octave \(currently set to \"$OCTAVE_BIN_PATH\", system version used, if left empty\)
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81 read OCTAVE_BIN_PATH
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82 if [ "$OCTAVE_BIN_PATH" == "" ];
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83 then
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84 OCTAVE_BIN_PATH=`which octave`
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85 if [ "$OCTAVE_BIN_PATH" == "" ];
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86 then
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87 echo octave not found
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88 exit -1
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89 fi
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90 fi
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91 echo '=>' Setting octave\'s path to \"$OCTAVE_BIN_PATH\"
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92 echo
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93 echo Please enter the full path to mkoctfile \(currently set to \"$OCTAVE_MKOCT\", system version used, if left empty\)
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94 read OCTAVE_MKOCT
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95 if [ "$OCTAVE_MKOCT" == "" ];
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96 then
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97 OCTAVE_MKOCT=`which mkoctfile`
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98 if [ "$OCTAVE_MKOCT" == "" ];
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99 then
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100 OCTAVE_MKOCT=$(dirname $OCTAVE_BIN_PATH)/mkoctfile
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101 if [ ! -f OCTAVE_MKOCT ];
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102 then
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103 echo mkoctfile not found
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104 exit -1
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105 fi
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106 fi
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107 fi
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108 echo '=>' Setting mkoctfile\'s path to \"$OCTAVE_MKOCT\"
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109 echo
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110 MATLAB_BIN_PATH=
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111 fi
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112 if [ "$INTERPRETER" == 'matlab' ];
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113 then
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114 echo Please enter the full path to matlab \(currently set to \"$MATLAB_BIN_PATH\", system version used, if left empty\)
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115 read MATLAB_BIN_PATH
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116 if [ "${MATLAB_BIN_PATH}" == "" ];
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117 then
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118 MATLAB_BIN_PATH=`which matlab`
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119 if [ "$MATLAB_BIN_PATH" == "" ];
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120 then
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121 echo matlab not found
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122 exit -1
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123 fi
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124 fi
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125 if [ ! -f $MATLAB_BIN_PATH ];
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126 then
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127 echo matlab not found
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128 exit -1
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129 fi
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130 echo '=>' Setting matlab\'s path to \"$MATLAB_BIN_PATH\"
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131 echo
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132 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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133 read MATLAB_MEX_PATH
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134 if [ "$MATLAB_MEX_PATH" == "" ];
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135 then
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136 MATLAB_MEX_PATH=`which mex`
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137 if [ "$MATLAB_MEX_PATH" == "" ];
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138 then
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139 echo mex not found
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140 exit -1
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141 fi
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142 fi
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143 if [ ! -f "$MATLAB_MEX_PATH" ];
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144 then
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145 echo mex not found
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146 exit -1
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147 fi
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148 echo '=>' Setting mex\' path to \"$MATLAB_MEX_PATH\"
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149 echo
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150 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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151 read MATLAB_INCLUDE_DIR
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152 if [ "$MATLAB_INCLUDE_DIR" == "" ];
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153 then
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154 MATLAB_INCLUDE_DIR=$(dirname $MATLAB_BIN_PATH)/../extern/include
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155 fi
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156 if [ ! -d "$MATLAB_INCLUDE_DIR" ];
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157 then
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158 echo matlab include dir not found
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159 exit -1
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160 fi
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161 echo '=>' Setting matlab\'s include directory to \"$MATLAB_INCLUDE_DIR\"
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162 echo
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163 OCTAVE_BIN_PATH=
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164 fi
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165
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166 cp -p bin/deseq_config.sh bin/deseq_config.sh.bk
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167 grep -v -e OCTAVE_BIN_PATH -e OCTAVE_MKOCT -e MATLAB_BIN_PATH -e MATLAB_MEX_PATH -e MATLAB_INCLUDE_DIR \
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168 -e DESEQ_PATH -e DESEQ_SRC_PATH -e DESEQ_BIN_PATH \
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169 -e INTERPRETER -e SAMTOOLS_DIR -e PYTHON_PATH -e SCIPY_PATH -e R_PATH -e $DESEQ_VERSION bin/deseq_config.sh.bk \
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170 > bin/deseq_config.sh
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171 echo
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172 echo
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173 echo generating config file
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174
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175 echo export DESEQ_VERSION=$DESEQ_VERSION >> bin/deseq_config.sh
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176 echo export DESEQ_PATH=$DESEQ_PATH >> bin/deseq_config.sh
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177 echo export DESEQ_SRC_PATH=${DESEQ_PATH}/src >> bin/deseq_config.sh
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178 echo export DESEQ_BIN_PATH=${DESEQ_PATH}/bin >> bin/deseq_config.sh
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179 echo export INTERPRETER=$INTERPRETER >> bin/deseq_config.sh
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180 echo export MATLAB_BIN_PATH=$MATLAB_BIN_PATH >> bin/deseq_config.sh
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181 echo export MATLAB_MEX_PATH=$MATLAB_MEX_PATH >> bin/deseq_config.sh
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182 echo export MATLAB_INCLUDE_DIR=$MATLAB_INCLUDE_DIR >> bin/deseq_config.sh
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183 echo export OCTAVE_BIN_PATH=$OCTAVE_BIN_PATH >> bin/deseq_config.sh
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184 echo export OCTAVE_MKOCT=$OCTAVE_MKOCT >> bin/deseq_config.sh
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185 echo export SAMTOOLS_DIR=$SAMTOOLS_DIR >> bin/deseq_config.sh
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186 echo export PYTHON_PATH=$PYTHON_PATH >> bin/deseq_config.sh
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187 echo export SCIPY_PATH=$SCIPY_PATH >> bin/deseq_config.sh
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188 echo export R_PATH=$R_PATH >> bin/deseq_config.sh
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189
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190 echo
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191 echo Done.
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192 echo
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