Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 11:866d22e60e60 draft

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Uploaded
author davidvanzessen
date Thu, 13 Nov 2014 10:33:04 -0500
parents 06777331fbd8
children 24a80d4eff0c
comparison
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10:06777331fbd8 11:866d22e60e60
4 outputDir=$3 4 outputDir=$3
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 selection=$7 9 filterproductive=$7
10 useD="false" 10 useD="false"
11 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then 11 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then
12 useD="true" 12 useD="true"
13 fi 13 fi
14 dir="$(cd "$(dirname "$0")" && pwd)" 14 dir="$(cd "$(dirname "$0")" && pwd)"
15 mkdir $3 15 mkdir $3
16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1 16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 2>&1
17 cp $dir/tabber.js $outputDir 17 cp $dir/tabber.js $outputDir
18 cp $dir/style.css $outputDir 18 cp $dir/style.css $outputDir
19 cp $dir/script.js $outputDir 19 cp $dir/script.js $outputDir
20 cp $dir/jquery-1.11.0.min.js $outputDir 20 cp $dir/jquery-1.11.0.min.js $outputDir
21 cp $dir/jquery.tablesorter.min.js $outputDir 21 cp $dir/jquery.tablesorter.min.js $outputDir