Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison combined.sh @ 2:bb8d5c67c129 draft

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Uploaded
author davidvanzessen
date Fri, 22 Nov 2013 08:12:40 -0500
parents 9b2567a3ecc9
children ba2ef103d26e
comparison
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1:9b2567a3ecc9 2:bb8d5c67c129
1 #!/bin/bash 1 #!/bin/bash
2 2
3 export IGDATA=/home/david/Galaxy/galaxy-dist/toolsheddependencies/igBlastn/1.0.0/davidvanzessen/igblast_human/1c64c977624e/ncbi-igblast-1.0.0/;
4
5 clonalType=${@:(-3):1}
3 html=${@:(-2):1} 6 html=${@:(-2):1}
4 imageDir=${@:(-1):1} 7 imageDir=${@:(-1):1}
5 dir="$(cd "$(dirname "$0")" && pwd)" 8 dir="$(cd "$(dirname "$0")" && pwd)"
6 fileCount=`expr $# - 2` 9 fileCount=`expr $# - 3`
7 array=("$@") 10 array=("$@")
8 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html 11 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
12 for var in "$@"
13 do
14 echo "$var" >> $html
15 done
9 echo "<tr><td>-----------------------------------</td></tr>" >> $html 16 echo "<tr><td>-----------------------------------</td></tr>" >> $html
10 limit=`expr $fileCount / 2` 17 limit=`expr $fileCount / 2`
11 18
12 function blastAndParse { 19 function blastAndParse {
13 echo "<tr><td>Starting blast of $2</td></tr>" >> $html 20 echo "<tr><td>Starting blast of $2</td></tr>" >> $html
55 62
56 inputFile=$PWD/merged.txt 63 inputFile=$PWD/merged.txt
57 outputFile=$html 64 outputFile=$html
58 outputDir=$imageDir 65 outputDir=$imageDir
59 mkdir $outputDir 66 mkdir $outputDir
60 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1 67 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
61 echo "<html>" > $outputFile 68 echo "<html>" > $outputFile
62 echo "<img src='VPlot.png'/>" >> $outputFile 69 echo "<img src='VPlot.png'/>" >> $outputFile
63 echo "<img src='DPlot.png'/>" >> $outputFile 70 echo "<img src='DPlot.png'/>" >> $outputFile
64 echo "<img src='JPlot.png'/>" >> $outputFile 71 echo "<img src='JPlot.png'/>" >> $outputFile
65 72
77 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 84 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
78 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 85 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
79 count=$((count+1)) 86 count=$((count+1))
80 done 87 done
81 echo "</table>" >> $outputFile 88 echo "</table>" >> $outputFile
89 echo "<h1>$clonalType</h1>" >> $outputFile
82 90
83 echo "</html>" >> $2 91 echo "</html>" >> $2
84
85
86 #r_wrapper.sh $in_file $out_file $out_file.files_path
87
88 echo "<tr><td>done</td></tr>" >> $html