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diff define_clones.sh @ 1:326165da9ece draft

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Uploaded
author davidvanzessen
date Thu, 04 Aug 2016 08:59:47 -0400
parents dda9b2e72e2b
children 6f57d43a1f4c
line wrap: on
line diff
--- a/define_clones.sh	Tue May 03 09:52:21 2016 -0400
+++ b/define_clones.sh	Thu Aug 04 08:59:47 2016 -0400
@@ -19,13 +19,21 @@
 	link=$8
 	dist=$9
 	output=${10}
+	output2=${11}
 	
-	/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	#/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	/home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
 else
 	method=$3
 	output=$4
+	output2=$5
 	
-	/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	#/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
+	
+	Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
 fi
 
 cp $PWD/outdir/output_clone-pass.tab $output