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annotate inSiliCow-run.sh @ 0:50112d3941d8 draft

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"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
author siwaa
date Mon, 07 Apr 2025 15:18:25 +0000
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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1 #!/bin/bash
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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2
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3 # Title: inSiliCow-run.sh
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4 # Address: main/run
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5 # Description: Launch simulations
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6 # Authors: Olivier MARTIN ( https://orcid.org/0000-0001-7375-2850 )
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7 # Pierre Blavy
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8 # Contact: olivier.martin-mosar@inrae.fr
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9 # Date: 2025
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10 # Usage: inSiliCow-run.sh example_xx [out]
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11 # example_xx is a folder in examples/
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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12 # out is the output folder, default ./out
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13
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14 clear
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16 #--------------------------------------
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17 #--- Colors for display in terminal ---
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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18 #--------------------------------------
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19
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20 # Set Bold High Intensity colors
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21 R='\033[1;91m' # Red
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22 B='\033[1;94m' # Blue
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23 NC='\033[0m' # No Color
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24
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25 #Set BIP sound
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26 BIP='\007'
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27
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28 # --- Opening message ---
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29 echo -e ${B}"\n> Launching inSiliCow"${NC}
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30
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31 # -----------------------
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32 # --- Input arguments ---
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33 # -----------------------
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34 #$1 is an example folder that exists in examples
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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35 #$2 is the output folder, must exists, default "./out"
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36
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37 if [ "$#" -le 0 ]; then
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38 echo -e ${B}"\n>> Missing argument"
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39 echo -e ">> Usage:"${NC}" inSilicow-run example_00 [out]"
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40 echo -e ${B}"\n>> Aborted\n"${NC}
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41 exit 1
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42 fi
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43
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44 INPUT_DIR=$(realpath "examples/$1" )
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45 OUTPUT_DIR=$(realpath ${2:-"./out"})
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46 mkdir -p $OUTPUT_DIR
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47
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48
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49 FARMER_LOG=$(realpath "examples/farmer-log.txt" )
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50 SCRIPTS_DIR=$(realpath ./)
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51 SCILAB=$(ls -drt $HOME/* | grep scilab- | tail -1)"/bin/scilab-cli"
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52 INSILICOW=$(realpath ./../insilicow-linux)
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53
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54 CURRENT=`pwd`
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55
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56 # --------------------------
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57 # --- Check things ---------
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58 # --------------------------
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59
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60 #Input does'nt exists => return
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61 if [ ! -d "$INPUT_DIR" ]; then
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62 echo -e ${BIP}${R}"\n>> Input directory $INPUT_DIR does not exist\n";
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63 echo -e ">> Aborted\n";
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64 exit 1;
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65 fi
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66
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67 #Output does'nt exists => return
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68 #if [ ! -d "$OUTPUT_DIR" ]; then
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69 # echo -e ${BIP}${R}"\n>> Output directory $OUTPUT_DIR does not exist\n";
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70 # echo -e ">> Aborted\n";
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71 # exit 1;
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72 #fi
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73
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74 #inSiliCow binary does'nt exists => return
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75 if [ ! -e "$INSILICOW" ]; then
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76 echo -e ${BIP}${R}"\n>> inSiliCow binary $INSILICOW does not exist\n";
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77 echo -e ">> Aborted\n";
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78 exit 1;
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79 fi
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80
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81 # -----------------------
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82 # --- Output ------------
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83 # -----------------------
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84
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85 #Get current date to name output folder
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86 d=`date "+%Y%m%d_%H%M%S_%N"`
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87 OUT_JOB="$OUTPUT_DIR/job-$d"
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88 ZIP_FILE=$(realpath "$OUTPUT_DIR/simulations-$d.zip" )
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89
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90 # ------------------------------
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91 # --- Print input and output ---
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92 # ------------------------------
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93
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94 echo -e ${B}"\n>> Pathways:"
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95 echo -e " Input:\t$INPUT_DIR";
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96 echo -e " Output:\t$OUT_JOB";
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97 echo -e " Scilab:\t$SCILAB";
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98 echo -e " inSiliCow:\t$INSILICOW\n"${NC};
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99
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100
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101 # ---------------------------------
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102 # --- Make output folders ---------
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103 # ---------------------------------
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104 mkdir -p "$OUT_JOB/in";
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105 mkdir -p "$OUT_JOB/out";
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106
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107 # -------------------------------------
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108 # --- check if scilab is responding ---
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109 # -------------------------------------
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110
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111 #check-scilab.sci xxx creates a file called "xxx/scilab_is_ok"
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112 rm -f "$OUTPUT_DIR/scilab_is_ok"
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113
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114 #"$SCILAB" -f "$SCRIPTS_DIR/check-scilab.sci" -nwni -quit -args "$OUTPUT_DIR";
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115
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116 #if [ ! -f "$OUTPUT_DIR/scilab_is_ok" ]; then
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117 # echo -e ${BIP}${R}"\n>> Scilab is not responding\n";
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118 # echo -e ">> Aborted\n";
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119 # exit 0;
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120 #fi
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121
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122 rm "$OUTPUT_DIR/scilab_is_ok"
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123
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124 # --------------------------
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125 # --- Run the jobs ---------
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126 # --------------------------
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127
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128 # --- Track time ---
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129 SECONDS=0;
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130
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131 #Format elapsed time
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132 FormatSeconds () {
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133 seconds="$1"
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134 date -ud @${seconds} +"$(( seconds/3600/24 ))d %Hh %Mm %Ss" \
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135 | sed -r 's/\b0([0-9])/\1/g; s/\b0(s|m|h|d)//g; s/ +/ /g; s/^ +//; s/ +$//; s/^$/0s/'
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136 }
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137
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138 #copy input to $OUT_JOB/in
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139 cp -r "$INPUT_DIR/"* "$OUT_JOB/in/"
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140 cp "$FARMER_LOG" "$OUT_JOB/in/"
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141
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142 echo -e ${B}"\n>> Starting job $d\n"${NC}
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143
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144 # --------------
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145 # --- explan ---
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146 # --------------
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147
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148 #Create file explan-config.txt with right paths
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149 cat > "$OUT_JOB/in/explan-config.txt" << EOF
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150 explan{
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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151 IN_CPU = 4 #number of parallel jobs
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152 IN_EXPLAN = $OUT_JOB/in/explan.txt
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153 OUT_FOLDER = $OUT_JOB/out/
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154 IN_FOLDER = $OUT_JOB/in/
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155 IN_EXE = $INSILICOW
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156 SCRIPT_FOLDER = $SCRIPTS_DIR
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157 OUT_FOLDER = $OUT_JOB/sim
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158 IN_SCILAB = $SCILAB
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159 }
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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160 EOF
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161
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162
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163 # Execute R script to launch simulations
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164 echo -e ${B}"\n>> Starting simulation\n"${NC}
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165 Rscript "$SCRIPTS_DIR/explan2.R" "$OUT_JOB/in/explan-config.txt"
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166
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167
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168 # ZIP
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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169
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170 #uncomment the block below to zip output
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171
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172 #rm -f "$ZIP_FILE"
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173 #echo -e ${B}"\n>> Compress simulation to $ZIP_FILE \n"${NC}
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174 #cd "$OUT_JOB" && \
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175 #zip -rq9 "$ZIP_FILE" ./ -x out/sim_*/log_herd.txt && \
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176 #cd "$CURRENT" && \
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177 #rm -rf "$OUT_JOB"
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178
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179
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180 # -----------------------------------
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181 # --- display final message ---------
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182 # -----------------------------------
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183
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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184 echo -e ${B}"\n>> Job "$d" done in $(FormatSeconds $SECONDS)${NC}\n"
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
parents:
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185