Loading launch_universc.sh +22 −4 Original line number Diff line number Diff line Loading @@ -1557,10 +1557,28 @@ if [[ $lock -eq 0 ]]; then if [[ $verbose ]]; then echo "restore cloupe" fi sed -i 's/#*#@include "_cloupe_stages.mro"/@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro sed -i '/output_for_cloupe/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## list cloupe output as (not null) sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## add cloupe to outputs sed -i '/out cloupe cloupe/ {s/^#*#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro #restore 11 lines for cloupe preprocess call (all following steps are needed to be called together or the call will break) ## restore defining CLOUPE_PREPROCESS 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/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## remove calling CLOUPE_PREPROCESS ### iterate over all files calling CLOUPE_PREPROCESS for file in $(grep -l "call CLOUPE_PREPROCES" /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/mro/*.mro ) do #find start of CLOUPE_PREPROCESS call num=$(grep -n "call CLOUPE_PREPROCESS" $file | head -n 1 | cut -d":" -f1) #find end of CLOUPE_PREPROCESS call num2=$(($num +$(tail -n $(echo $(($(wc -l $file | cut -f1 -d " ") - $num))) $file | grep -n ")" | head -n 1 | cut -d":" -f1))) if [[ $verbose ]]; then echo "lines ${num}-${num2} restored in $file" fi eval "sed -i '$(echo "${num},${num2}s/^#*#//g")' $file" done elif [[ $lastcall_p == "default:10x" ]] || [[ ! -f $lastcallfile ]]; then #disable cloupe generation if [[ $verbose ]]; then Loading @@ -1570,7 +1588,7 @@ if [[ $lock -eq 0 ]]; then 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 folowing steps are needed to be suppressed together or call will break) #remove 11 lines for cloupe preprocess call (all following steps are needed to be suppressed together or call will break) ## remove defining CLOUPE_PREPROCESS sed -i 's/@include "_cloupe_stages.mro"/#@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## remove listing CLOUPE in output Loading Loading
launch_universc.sh +22 −4 Original line number Diff line number Diff line Loading @@ -1557,10 +1557,28 @@ if [[ $lock -eq 0 ]]; then if [[ $verbose ]]; then echo "restore cloupe" fi sed -i 's/#*#@include "_cloupe_stages.mro"/@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro sed -i '/output_for_cloupe/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## list cloupe output as (not null) sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS\.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## add cloupe to outputs sed -i '/out cloupe cloupe/ {s/^#*#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro sed -i '/output_for_cloupe/s/null/CLOUPE_PREPROCESS.output_for_cloupe/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro #restore 11 lines for cloupe preprocess call (all following steps are needed to be called together or the call will break) ## restore defining CLOUPE_PREPROCESS 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/s/^#*#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## remove calling CLOUPE_PREPROCESS ### iterate over all files calling CLOUPE_PREPROCESS for file in $(grep -l "call CLOUPE_PREPROCES" /home/tom/local/bin/cellranger-3.0.2/cellranger-cs/3.0.2/mro/*.mro ) do #find start of CLOUPE_PREPROCESS call num=$(grep -n "call CLOUPE_PREPROCESS" $file | head -n 1 | cut -d":" -f1) #find end of CLOUPE_PREPROCESS call num2=$(($num +$(tail -n $(echo $(($(wc -l $file | cut -f1 -d " ") - $num))) $file | grep -n ")" | head -n 1 | cut -d":" -f1))) if [[ $verbose ]]; then echo "lines ${num}-${num2} restored in $file" fi eval "sed -i '$(echo "${num},${num2}s/^#*#//g")' $file" done elif [[ $lastcall_p == "default:10x" ]] || [[ ! -f $lastcallfile ]]; then #disable cloupe generation if [[ $verbose ]]; then Loading @@ -1570,7 +1588,7 @@ if [[ $lock -eq 0 ]]; then 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 folowing steps are needed to be suppressed together or call will break) #remove 11 lines for cloupe preprocess call (all following steps are needed to be suppressed together or call will break) ## remove defining CLOUPE_PREPROCESS sed -i 's/@include "_cloupe_stages.mro"/#@include "_cloupe_stages.mro"g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro ## remove listing CLOUPE in output Loading
