Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 22:2555b94dbdb2 draft

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Uploaded
author davidvanzessen
date Thu, 15 Jan 2015 09:16:19 -0500
parents b79ad381ced0
children 5f0597a3fd8b
comparison
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21:2424111b9198 22:2555b94dbdb2
5 outputFile=$3/index.html #$2 5 outputFile=$3/index.html #$2
6 clonalType=$4 6 clonalType=$4
7 species=$5 7 species=$5
8 locus=$6 8 locus=$6
9 filterproductive=$7 9 filterproductive=$7
10 dir="$(cd "$(dirname "$0")" && pwd)"
10 useD="false" 11 useD="false"
11 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then 12 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
12 useD="true" 13 useD="true"
13 fi 14 fi
14 dir="$(cd "$(dirname "$0")" && pwd)"
15 mkdir $3 15 mkdir $3
16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 2>&1 16 cp $dir/genes.txt $outputDir
17 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1
17 cp $dir/tabber.js $outputDir 18 cp $dir/tabber.js $outputDir
18 cp $dir/style.css $outputDir 19 cp $dir/style.css $outputDir
19 cp $dir/script.js $outputDir 20 cp $dir/script.js $outputDir
20 cp $dir/jquery-1.11.0.min.js $outputDir 21 cp $dir/jquery-1.11.0.min.js $outputDir
21 samples=`cat $outputDir/samples.txt` 22 samples=`cat $outputDir/samples.txt`