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33
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1 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18}
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32
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2
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34
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3 #get tool data and tool install directories
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4 tooldir=$(cut -d';' -f1 <<< ${12})
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5 tooldata=$(cut -d';' -f2 <<< ${12})
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6
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2
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7 #create temp directory for row and col order and dendro files.
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34
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8 tdir=$tooldata/$(date +%y%m%d%M%S)
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2
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9 echo $tdir
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10 mkdir $tdir
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32
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11
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2
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12 #run R to cluster matrix
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34
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13 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
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2
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14 rc=$?;
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15 if [ $rc != 0 ]
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16 then
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17 echo $output;
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18 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
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19 then
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20 echo "";
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21 echo "Note: This error can occur when there is no variation in a row or column. Try a different distance measure or remove rows/columns without variation.";
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33
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22 echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix. Check your Input Matrix entry.";
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2
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23 fi
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24 exit $rc;
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25 fi
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26
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27 #there are a variable number of triplicate parameters for classification bars
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28 count=0
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29 classifications=''
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30
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31 #if row cut was done, add that autogenerated classification
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33
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32 if [ ${13} -gt 1 ]
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2
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33 then
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34 classifications="Class $tdir/ROfile.txt.cut row_categorical"
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35 fi
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36
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37 #if col cut was done, add that autogenerated classification
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33
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38 if [ ${14} -gt 1 ]
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2
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39 then
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40 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
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41 fi
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42
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43 #now add the user provided classification files
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44 for i in "$@"; do
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33
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45 if [ $count -gt 16 ]
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2
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46 then
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47 classifications=$classifications' '$i
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48 fi
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49 count=$((count+1))
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50 done
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33
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51 echo "classifications " $classifications
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52 echo "${11} " ${11}
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2
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53 #call java program to generate NGCHM viewer files.
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34
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54 java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt ${11} $classifications
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2
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55 #clean up tempdir
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56 rm -rf $tdir
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