correct restoring cloupe outputs for 10x (da321b5a) · Commits · github_fork / Universc

launch_universc.sh

+5 −5

Original line number	Diff line number	Diff line
		@@ -1559,9 +1559,9 @@ if [[ $lock -eq 0 ]]; then
		fi
		## list cloupe output as (not null)
		if [[ $verbose ]]; then
		echo "sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"
		echo "sed -i '/cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"
		fi
		sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		sed -i '/cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		## add cloupe to outputs
		if [[ $verbose ]]; then
		echo "sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro"
		@@ -1572,7 +1572,7 @@ if [[ $lock -eq 0 ]]; then
		if [[ $verbose ]]; then
		echo "sed -i 's/^##@include "_cloupe_stages.mro"/@include "_cloupe_stages.mro"/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro"
		fi
		sed -i 's/^##@include "_cloupe_stages.mro"/@include "_cloupe_stages.mro"g/' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i 's/^##@include "_cloupe_stages.mro"/@include "_cloupe_stages.mro"/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		## remove listing CLOUPE in output
		sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		## remove calling CLOUPE_PREPROCESS
		@@ -1593,8 +1593,6 @@ if [[ $lock -eq 0 ]]; then
		if [[ $verbose ]]; then
		echo "disable cloupe"
		fi
		## list cloupe output as null
		sed -i '/output_for_cloupe/s/CLOUPE_PREPROCESS\.output_for_cloupe/null/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		## remove cloupe from outputs
		sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		#remove 11 lines for cloupe preprocess call (all following steps are needed to be suppressed together or call will break)
		@@ -1602,6 +1600,8 @@ if [[ $lock -eq 0 ]]; then
		sed -i 's/@include "_cloupe_stages.mro"/#@include "_cloupe_stages.mro"/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		## remove listing CLOUPE in output
		sed -i '/output_for_cloupe/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		## list cloupe output as null
		sed -i '/output_for_cloupe/s/CLOUPE_PREPROCESS\.output_for_cloupe/null/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		## remove calling CLOUPE_PREPROCESS
		### iterate over all files calling CLOUPE_PREPROCESS
		for file in $(grep -l "call CLOUPE_PREPROCESS" /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/mro/*.mro )

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