Loading launch_universc.sh +10 −0 Original line number Diff line number Diff line Loading @@ -1957,6 +1957,8 @@ if [[ $lock -eq 0 ]]; then else old_umi_length=$lastcall_u fi old_rna_offset=`echo $((${lastcall_b}+${last_call_u}))` new_rna_offset=`echo $((${barcodelength}+${umilength}))` # convert barcodes back if last technology barcode greater than 16 bp if [[ $old_bc_length -gt 16 ]]; then sed -i "s/\'barcode_read_length\': ${old_bc_length},/\'barcode_read_length\': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py Loading @@ -1966,6 +1968,10 @@ if [[ $lock -eq 0 ]]; then if [[ $old_umi_length -gt 12 ]]; then sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi if [[ $old_rna_offset -gt 26 ]]; then sed -i "s/\'rna_read_offset\': ${old_rna_offset},/\'rna_read_offset\': 26,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi # convert barcodes if new technology greater than 16 bp if [[ $minlength -gt 16 ]]; then sed -i "s/\'barcode_read_length\': 16,/\'barcode_read_length\': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py Loading @@ -1975,6 +1981,10 @@ if [[ $lock -eq 0 ]]; then if [[ $umilength -gt 12 ]]; then sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi if [[ $ new_rna_offset -gt 26 ]]; then sed -i "s/\'rna_read_offset\': 26,/\'rna_read_offset\': ${new_rna_offset},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi echo " ${cellrangerpath} set for $technology" Loading Loading
launch_universc.sh +10 −0 Original line number Diff line number Diff line Loading @@ -1957,6 +1957,8 @@ if [[ $lock -eq 0 ]]; then else old_umi_length=$lastcall_u fi old_rna_offset=`echo $((${lastcall_b}+${last_call_u}))` new_rna_offset=`echo $((${barcodelength}+${umilength}))` # convert barcodes back if last technology barcode greater than 16 bp if [[ $old_bc_length -gt 16 ]]; then sed -i "s/\'barcode_read_length\': ${old_bc_length},/\'barcode_read_length\': 16,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py Loading @@ -1966,6 +1968,10 @@ if [[ $lock -eq 0 ]]; then if [[ $old_umi_length -gt 12 ]]; then sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi if [[ $old_rna_offset -gt 26 ]]; then sed -i "s/\'rna_read_offset\': ${old_rna_offset},/\'rna_read_offset\': 26,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/\'umi_read_length\': ${old_umi_length},/\'umi_read_length\': 10/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi # convert barcodes if new technology greater than 16 bp if [[ $minlength -gt 16 ]]; then sed -i "s/\'barcode_read_length\': 16,/\'barcode_read_length\': ${minlength},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py Loading @@ -1975,6 +1981,10 @@ if [[ $lock -eq 0 ]]; then if [[ $umilength -gt 12 ]]; then sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi if [[ $ new_rna_offset -gt 26 ]]; then sed -i "s/\'rna_read_offset\': 26,/\'rna_read_offset\': ${new_rna_offset},/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py sed -i "s/\'umi_read_length\': 10,/\'umi_read_length\': ${umilength}/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py fi echo " ${cellrangerpath} set for $technology" Loading
