# HG changeset patch
# User davidvanzessen
# Date 1549355201 18000
# Node ID c787e79e8b90d21353da1e5c80b20a25dc78999a
# Parent  2649a821162dbbe29d7128a70c8aa615cf85c81c
Uploaded

diff -r 2649a821162d -r c787e79e8b90 change_o/define_clones.sh
--- a/change_o/define_clones.sh	Thu Jan 31 05:53:59 2019 -0500
+++ b/change_o/define_clones.sh	Tue Feb 05 03:26:41 2019 -0500
@@ -21,9 +21,7 @@
 	output=${10}
 	output2=${11}
 	
-	python3 $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
+	DefineClones.py -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
@@ -31,9 +29,7 @@
 	output=$4
 	output2=$5
 	
-	python3 $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
+	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 2649a821162d -r c787e79e8b90 change_o/makedb.sh
--- a/change_o/makedb.sh	Thu Jan 31 05:53:59 2019 -0500
+++ b/change_o/makedb.sh	Tue Feb 05 03:26:41 2019 -0500
@@ -29,9 +29,7 @@
 
 echo "makedb: $PWD/outdir"
 
-python3 $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
+MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
 
 mv $PWD/outdir/output_db-pass.tab $output
 
diff -r 2649a821162d -r c787e79e8b90 shm_csr.xml
--- a/shm_csr.xml	Thu Jan 31 05:53:59 2019 -0500
+++ b/shm_csr.xml	Tue Feb 05 03:26:41 2019 -0500
@@ -9,6 +9,7 @@
 		<requirement type="package" version="0.5.0">r-scales</requirement>
 		<requirement type="package" version="3.4_5">r-seqinr</requirement>
 		<requirement type="package" version="1.11.4">r-data.table</requirement>
+		<requirement type="package" version="0.4.5">changeo</requirement>
 	</requirements>
 	<command interpreter="bash">
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
diff -r 2649a821162d -r c787e79e8b90 wrapper.sh
--- a/wrapper.sh	Thu Jan 31 05:53:59 2019 -0500
+++ b/wrapper.sh	Tue Feb 05 03:26:41 2019 -0500
@@ -72,7 +72,7 @@
 echo "---------------- class identification ----------------"
 echo "---------------- class identification ----------------<br />" >> $log
 
-python2 $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
+python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
 
 echo "---------------- merge_and_filter.r ----------------"
 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
@@ -198,7 +198,7 @@
 echo "---------------- shm_csr.py ----------------"
 echo "---------------- shm_csr.py ----------------<br />" >> $log
 
-python2 $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
+python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
 
 echo "---------------- aa_histogram.r ----------------"
 echo "---------------- aa_histogram.r ----------------<br />" >> $log