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1
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1 #echo "1: " $1
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2 #echo "2: " $2
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3 #echo "3: " $3
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4 #echo "4: " $4
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5 #echo "5: " $5
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6 #echo "6: " $6
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7 #echo "7: " $7
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8 #echo "8: " $8
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9 #echo "9: " $9
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10 #echo "10: " ${10}
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11 #echo "11: " ${11}
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12 #echo "12: " ${12}
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13 #echo "13: " ${13}
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14 #echo "14: " ${14}
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15 #echo "15: " ${15}
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16 #echo "16: " ${16}
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17 #echo "17: " ${17}
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18 #echo "18: " ${18}
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19 #echo "19: " ${19}
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20 #echo "20: " ${20}
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21 #echo "21: " ${21}
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22 #echo "22: " ${22}
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23 #echo "23: " ${23}
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24 #echo "23: " ${24}
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25 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23}
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0
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26
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2
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27 #get tool data and tool install directories
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28 tooldir=$(cut -d';' -f1 <<< ${12})
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29 tooldata=$(cut -d';' -f2 <<< ${12})
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30
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0
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31 #create temp directory for row and col order and dendro files.
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2
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32 tdir=$tooldata/$(date +%y%m%d%M%S)
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0
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33 echo $tdir
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34 mkdir $tdir
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35 #run R to cluster matrix
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2
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36 output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
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0
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37 rc=$?;
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38 if [ $rc != 0 ]
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39 then
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40 echo $output;
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41 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
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42 then
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43 echo "";
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44 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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1
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45 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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0
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46 fi
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47 exit $rc;
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48 fi
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1
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49
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0
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50 #there are a variable number of triplicate parameters for classification bars
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51 count=0
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52 classifications=''
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53
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54 #if row cut was done, add that autogenerated classification
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1
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55 if [ ${13} -gt 1 ]
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0
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56 then
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1
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57 classifications="Class $tdir/ROfile.txt.cut row_categorical color_plot"
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0
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58 fi
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59
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60 #if col cut was done, add that autogenerated classification
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1
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61 if [ ${14} -gt 1 ]
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0
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62 then
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1
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63 classifications="$classifications Class $tdir/COfile.txt.cut col_categorical color_plot"
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0
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64 fi
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65
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66 #now add the user provided classification files
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67 for i in "$@"; do
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1
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68 if [ $count -gt 20 ]
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0
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69 then
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1
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70 # echo "class entry: " $i
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0
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71 classifications=$classifications' '$i
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72 fi
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73 count=$((count+1))
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74 done
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1
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75 #echo "classifications: " $classifications
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76
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0
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77 #call java program to generate NGCHM viewer files.
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2
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78 java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt "${17}" "${19}" $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt "${18}" "${20}" ${11} "${21}" $classifications
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0
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79 #clean up tempdir
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80 rm -rf $tdir
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