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0
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1 echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15}
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2
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3 #create temp directory for row and col order and dendro files.
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4 tdir=${11}/$(date +%s)
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5 echo $tdir
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6 mkdir $tdir
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7
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8 #run R to cluster matrix
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9 output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt)"
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10 rc=$?; if [[ $rc != 0 ]]; then echo $output; exit $rc; fi
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11
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12
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13 #there are a variable number of triplicate parameters for classification bars
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14 count=0
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15 classifcations=''
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16
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17 for i in "$@"; do
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18 if [ $count -gt 10 ]
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19 then
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20 classifications=$classifications' '$i
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21 fi
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22
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23 count=$((count+1))
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24 done
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25
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26 #call java program to generate NGCHM viewer files.
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27 java -jar ${11}/GalaxyMapGen.jar $1 $2 DataLayer1 $3 linear Row Column $4 $5 $6 $tdir/ROfile.txt $tdir/RDfile.txt $7 $8 $9 $tdir/COfile.txt $tdir/CDfile.txt ${10} $classifications
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28
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29 #clean up tempdir
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30 rm -rf $tdir
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