Loading launch_universc.sh +18 −0 Original line number Diff line number Diff line Loading @@ -1466,6 +1466,7 @@ if [[ $verbose ]]; then echo " setting whitelist barcode file." fi custombarcodes=false if [[ -n "$barcodefile" ]]; then if [[ ! -f $barcodefile ]]; then echo "Error: File selected for option --barcodefile does not exist" Loading @@ -1473,6 +1474,7 @@ if [[ -n "$barcodefile" ]]; then else #getting absolute path barcodefile=$(readlink -f $barcodefile) custombarcodes=true #allowing WellList from ICELL8 and other well-based techniques if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "custom" ]]; then seg=$'\t' Loading Loading @@ -1947,6 +1949,22 @@ if [[ $lock -eq 0 ]]; then eval "sed -i '$(echo "${num},${num2}s/^/#/g")' $file" done fi #check for custom whitelist if [[ $custombarcodes == "true" ]]; then #disable detect chemistry check for custom whitelist if [[ $verbose ]]; then echo "disable detect chemistry check..." fi sed -i "s/ raise NoChemistryFoundException/ return best_chem #raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/ (100\.0 \* best_frac/ #(100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py else if [[ $verbose ]]; then echo "restore detect chemistry check..." fi #restore detect chemistry check for custom whitelist sed -i "s/ return best_chem \#raise NoChemistryFoundException/ raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/ \#(100\.0 \* best_frac/ (100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi echo " ${cellrangerpath} set for $technology" #whitelist file name Loading Loading
launch_universc.sh +18 −0 Original line number Diff line number Diff line Loading @@ -1466,6 +1466,7 @@ if [[ $verbose ]]; then echo " setting whitelist barcode file." fi custombarcodes=false if [[ -n "$barcodefile" ]]; then if [[ ! -f $barcodefile ]]; then echo "Error: File selected for option --barcodefile does not exist" Loading @@ -1473,6 +1474,7 @@ if [[ -n "$barcodefile" ]]; then else #getting absolute path barcodefile=$(readlink -f $barcodefile) custombarcodes=true #allowing WellList from ICELL8 and other well-based techniques if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq" ]] || [[ "$technology" == "custom" ]]; then seg=$'\t' Loading Loading @@ -1947,6 +1949,22 @@ if [[ $lock -eq 0 ]]; then eval "sed -i '$(echo "${num},${num2}s/^/#/g")' $file" done fi #check for custom whitelist if [[ $custombarcodes == "true" ]]; then #disable detect chemistry check for custom whitelist if [[ $verbose ]]; then echo "disable detect chemistry check..." fi sed -i "s/ raise NoChemistryFoundException/ return best_chem #raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/ (100\.0 \* best_frac/ #(100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py else if [[ $verbose ]]; then echo "restore detect chemistry check..." fi #restore detect chemistry check for custom whitelist sed -i "s/ return best_chem \#raise NoChemistryFoundException/ raise NoChemistryFoundException/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/ \#(100\.0 \* best_frac/ (100.0 * best_frac/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi echo " ${cellrangerpath} set for $technology" #whitelist file name Loading
