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3
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1 #!/bin/bash
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2
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3 analyseType=$1;
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4 out1=$2;
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5 out2=$3;
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6 out3=$4;
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7 log1=$5;
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8 galaxyOutDir=$6;
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9
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10 version=$(java -version 2>&1 | grep version)
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11 if [[ ! $version =~ 1.8 ]]; then
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12 echo "Java found: $version. Tassel 5.0 requires java 1.8..." >&2
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13 exit 1
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14 fi
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15
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16 mkdir $galaxyOutDir
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17
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18 # Suppression des 6 premiers arguments de la liste des arguments $@
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19 shift; shift; shift; shift; shift; shift;
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20
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21
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22 if [[ $analyseType == glm ]]
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23 then
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24 run_pipeline.pl $* >> $log1 2>&1
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25 mv "$galaxyOutDir/TASSELGLM1.txt" $out1
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26 mv "$galaxyOutDir/TASSELGLM2.txt" $out2
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27 fi
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28
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29 if [[ $analyseType == mlm ]]
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30 then
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31 run_pipeline.pl $* >> $log1 2>&1
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32 mv "$galaxyOutDir/TASSELMLM1.txt" $out1
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33 mv "$galaxyOutDir/TASSELMLM2.txt" $out2
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34 mv "$galaxyOutDir/TASSELMLM3.txt" $out3
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35 fi
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36
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37 if [[ $analyseType == ld ]]
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38 then
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39 run_pipeline.pl $* >> $log1 2>&1
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40 fi
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41
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42
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43 if [[ $analyseType == ck ]]
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44 then
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45 run_pipeline.pl $* >> $log1 2>&1
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46 mv "$galaxyOutDir/kinship.txt" $out1
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47 fi
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