# HG changeset patch
# User davidvanzessen
# Date 1470915636 14400
# Node ID 6f57d43a1f4c7462a80d7f17181d16222ae1d4d6
# Parent  326165da9ece53559ebde307d511b35d29bbc1b5
Uploaded

diff -r 326165da9ece -r 6f57d43a1f4c create_germlines.sh
--- a/create_germlines.sh	Thu Aug 04 08:59:47 2016 -0400
+++ b/create_germlines.sh	Thu Aug 11 07:40:36 2016 -0400
@@ -16,7 +16,7 @@
 
 mkdir $PWD/outdir
 
-/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
-#/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
+#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
+/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned
 
 mv $PWD/outdir/output_germ-pass.tab $output
diff -r 326165da9ece -r 6f57d43a1f4c define_clones.sh
--- a/define_clones.sh	Thu Aug 04 08:59:47 2016 -0400
+++ b/define_clones.sh	Thu Aug 11 07:40:36 2016 -0400
@@ -21,8 +21,8 @@
 	output=${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
-	/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
+	/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
@@ -30,8 +30,8 @@
 	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
-	/home/galaxy/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
diff -r 326165da9ece -r 6f57d43a1f4c makedb.sh
--- a/makedb.sh	Thu Aug 04 08:59:47 2016 -0400
+++ b/makedb.sh	Thu Aug 11 07:40:36 2016 -0400
@@ -27,7 +27,7 @@
 
 mkdir $PWD/outdir
 
-#/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
-/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
+#/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
 
 mv $PWD/outdir/output_db-pass.tab $output