Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 50:8ba6afa1247a draft

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Uploaded
author davidvanzessen
date Thu, 28 Jan 2016 09:21:25 -0500
parents 5c6b9e99d576
children d3542f87a304
line wrap: on
line diff
--- a/wrapper.sh	Wed Nov 18 05:55:04 2015 -0500
+++ b/wrapper.sh	Thu Jan 28 09:21:25 2016 -0500
@@ -147,7 +147,8 @@
 if [[ "$naive_output" != "None" ]]
 then
 	echo "naive_output: $naive_output"
-	python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
+	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
+	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1
 	Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
 fi