Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison heatmap_advanced.sh @ 2:19382473a76b draft
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author | insilico-bob |
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date | Thu, 08 Feb 2018 14:47:49 -0500 |
parents | 603f99d9e776 |
children | 1f13d304ddbd |
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1:603f99d9e776 | 2:19382473a76b |
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22 #echo "22: " ${22} | 22 #echo "22: " ${22} |
23 #echo "23: " ${23} | 23 #echo "23: " ${23} |
24 #echo "23: " ${24} | 24 #echo "23: " ${24} |
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} | 25 #echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23} |
26 | 26 |
27 #get tool data and tool install directories | |
28 tooldir=$(cut -d';' -f1 <<< ${12}) | |
29 tooldata=$(cut -d';' -f2 <<< ${12}) | |
30 | |
27 #create temp directory for row and col order and dendro files. | 31 #create temp directory for row and col order and dendro files. |
28 tdir=${12}/$(date +%y%m%d%M%S) | 32 tdir=$tooldata/$(date +%y%m%d%M%S) |
29 echo $tdir | 33 echo $tdir |
30 mkdir $tdir | 34 mkdir $tdir |
31 #run R to cluster matrix | 35 #run R to cluster matrix |
32 output="$(R --slave --vanilla --file=${12}/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} ${16} 2>&1)" | 36 output="$(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} ${16} 2>&1)" |
33 rc=$?; | 37 rc=$?; |
34 if [ $rc != 0 ] | 38 if [ $rc != 0 ] |
35 then | 39 then |
36 echo $output; | 40 echo $output; |
37 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] | 41 if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ] |
69 count=$((count+1)) | 73 count=$((count+1)) |
70 done | 74 done |
71 #echo "classifications: " $classifications | 75 #echo "classifications: " $classifications |
72 | 76 |
73 #call java program to generate NGCHM viewer files. | 77 #call java program to generate NGCHM viewer files. |
74 java -jar ${12}/GalaxyMapGen.jar "${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 | 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 |
75 #clean up tempdir | 79 #clean up tempdir |
76 rm -rf $tdir | 80 rm -rf $tdir |