Mercurial > repos > davidvanzessen > report_clonality_igg
diff r_wrapper.sh @ 22:2555b94dbdb2 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 15 Jan 2015 09:16:19 -0500 |
| parents | b79ad381ced0 |
| children | 5f0597a3fd8b |
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--- a/r_wrapper.sh Mon Jan 12 11:06:49 2015 -0500 +++ b/r_wrapper.sh Thu Jan 15 09:16:19 2015 -0500 @@ -7,13 +7,14 @@ species=$5 locus=$6 filterproductive=$7 +dir="$(cd "$(dirname "$0")" && pwd)" useD="false" -if [[ "$species" == "human" && "$locus" = "igh" ]] ; then +if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then useD="true" fi -dir="$(cd "$(dirname "$0")" && pwd)" mkdir $3 -Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 2>&1 +cp $dir/genes.txt $outputDir +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1 cp $dir/tabber.js $outputDir cp $dir/style.css $outputDir cp $dir/script.js $outputDir