Loading launch_universc.sh +16 −13 Original line number Diff line number Diff line Loading @@ -733,7 +733,7 @@ if [[ $setup == "true" ]]; then if [[ $technology == "10x" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi Loading @@ -742,7 +742,7 @@ if [[ $setup == "true" ]]; then #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading @@ -763,7 +763,7 @@ if [[ $setup == "true" ]]; then fi elif [[ $technology == "nadia" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi Loading @@ -789,7 +789,7 @@ if [[ $setup == "true" ]]; then #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading Loading @@ -821,15 +821,18 @@ if [[ $setup == "true" ]]; then fi elif [[ $technology == "icell8" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi #create a file with every possible barcode (permutation) if [[ -f iCELL8_barcode.txt.gz ]]; then rm iCELL8_barcode.txt.gz iCELL8_barcode.txt if [[ -f iCell8_barcode.txt.gz ]]; then rm iCell8_barcode.txt.gz fi if [[ ! -f iCELL8_barcode.txt ]]; then if [[ -f iCell8_barcode.txt ]]; then rm iCell8_barcode.txt fi if [[ ! -f iCell8_barcode.txt ]]; then #copy known iCell8 barcodes from convert repo to cellranger install rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/iCell8_barcode.txt #convert barcode whitelist to match converted barcodes Loading @@ -843,12 +846,12 @@ if [[ $setup == "true" ]]; then cp 737K-august-2016.txt 737K-august-2016.txt.backup fi #replace 10x barcodes with icell8 cat iCELL8_barcode.txt | sort | uniq > 737K-august-2016.txt cat iCell8_barcode.txt | sort | uniq > 737K-august-2016.txt echo " whitelist converted for iCELL8 compatibility with version 2 kit." #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading @@ -859,10 +862,10 @@ if [[ $setup == "true" ]]; then gzip 3M-february-2018.txt.backup fi #combine 10x and Nadia barcodes if [[ ! -f iCELL8_barcode.txt.gz ]]; then rm iCELL8_barcode.txt.gz if [[ ! -f iCell8_barcode.txt.gz ]]; then rm iCell8_barcode.txt.gz fi cat iCELL8_barcode.txt > 3M-february-2018.txt cat iCell8_barcode.txt > 3M-february-2018.txt gzip -f 3M-february-2018.txt echo " whitelist converted for iCELL8 compatibility with version 3 kit." fi Loading Loading
launch_universc.sh +16 −13 Original line number Diff line number Diff line Loading @@ -733,7 +733,7 @@ if [[ $setup == "true" ]]; then if [[ $technology == "10x" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi Loading @@ -742,7 +742,7 @@ if [[ $setup == "true" ]]; then #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading @@ -763,7 +763,7 @@ if [[ $setup == "true" ]]; then fi elif [[ $technology == "nadia" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi Loading @@ -789,7 +789,7 @@ if [[ $setup == "true" ]]; then #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading Loading @@ -821,15 +821,18 @@ if [[ $setup == "true" ]]; then fi elif [[ $technology == "icell8" ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 2 kit ..." cp 737K-august-2016.txt.backup 737K-august-2016.txt fi #create a file with every possible barcode (permutation) if [[ -f iCELL8_barcode.txt.gz ]]; then rm iCELL8_barcode.txt.gz iCELL8_barcode.txt if [[ -f iCell8_barcode.txt.gz ]]; then rm iCell8_barcode.txt.gz fi if [[ ! -f iCELL8_barcode.txt ]]; then if [[ -f iCell8_barcode.txt ]]; then rm iCell8_barcode.txt fi if [[ ! -f iCell8_barcode.txt ]]; then #copy known iCell8 barcodes from convert repo to cellranger install rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/iCell8_barcode.txt #convert barcode whitelist to match converted barcodes Loading @@ -843,12 +846,12 @@ if [[ $setup == "true" ]]; then cp 737K-august-2016.txt 737K-august-2016.txt.backup fi #replace 10x barcodes with icell8 cat iCELL8_barcode.txt | sort | uniq > 737K-august-2016.txt cat iCell8_barcode.txt | sort | uniq > 737K-august-2016.txt echo " whitelist converted for iCELL8 compatibility with version 2 kit." #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then #restore 10x barcodes if scripts has already been run (allows changing Nadia to iCELL8) if [[ -f nadia_barcode.txt ]] || [[ -f iCELL8_barcode.txt ]]; then if [[ -f nadia_barcode.txt ]] || [[ -f iCell8_barcode.txt ]]; then echo " restoring 10x barcodes for version 3 kit ..." cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz fi Loading @@ -859,10 +862,10 @@ if [[ $setup == "true" ]]; then gzip 3M-february-2018.txt.backup fi #combine 10x and Nadia barcodes if [[ ! -f iCELL8_barcode.txt.gz ]]; then rm iCELL8_barcode.txt.gz if [[ ! -f iCell8_barcode.txt.gz ]]; then rm iCell8_barcode.txt.gz fi cat iCELL8_barcode.txt > 3M-february-2018.txt cat iCell8_barcode.txt > 3M-february-2018.txt gzip -f 3M-february-2018.txt echo " whitelist converted for iCELL8 compatibility with version 3 kit." fi Loading
