minimized redundancy in the setup section. (83923766) · Commits · github_fork / Universc

launch_universc.sh

+64 −112

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ if [[ -z $cellrangerpass ]]; then
		echo "cellranger command is not found."
		exit 1
		fi
		ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.2.0.900333) \| head -n 3 \| tail -n 2`
		ver_info=`paste -d "\n" <(cellranger count --version) <(echo conversion script version 0.2.1) \| head -n 3 \| tail -n 2`
		##########


		@@ -509,9 +509,7 @@ if [[ $lastcall != $technology ]]; then
		fi

		#check if convertion is needs to be run before analysis (potentially overriding the user input)
		if [[ $technology == "10x" ]]; then
		convert=false
		elif [[ ! -d $crIN ]] \|\| [[ $lastcall != $technology ]]; then
		if [[ ! -d $crIN ]] \|\| [[ $lastcall != $technology ]]; then
		convert=true
		fi

		@@ -620,6 +618,8 @@ echo ""
		#run setup if called
		if [[ $setup == "true" ]]; then
		echo "setup begin"
		echo "updating barcodes in $barcodefolder for cellranger version $VERSION installed in $DIR ..."

		if [[ ! -w $barcodefolder ]]; then
		echo "Error: launch_universc.sh can only be run cellranger installed locally"
		echo "Running cellranger installed at $DIR"
		@@ -632,13 +632,11 @@ if [[ $setup == "true" ]]; then

		cd $barcodefolder

		#compressing v3 whilelist
		if [[ -f 3M-february-2018.txt ]]; then
		gzip -f 3M-february-2018.txt
		fi

		echo "updating barcodes in $barcodefolder for cellranger version $VERSION installed in $DIR ..."

		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
		echo " restoring 10x barcodes for version 2 kit ..."
		@@ -646,6 +644,7 @@ if [[ $setup == "true" ]]; then
		fi
		echo " whitelist converted for 10x compatibility with version 2 kit."

		if [[ $technology == "10x" ]]; 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)
		@@ -668,97 +667,46 @@ if [[ $setup == "true" ]]; then
		else
		echo " $DIR ready for $technology"
		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
		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 nadia_barcode.txt.gz ]]; then
		if [[ ! -f nadia_barcode.txt ]]; then
		gunzip nadia_barcode.txt.gz
		fi
		fi
		if [[ ! -f nadia_barcode.txt ]]; then
		echo " generating expected barcodes for Nadia ..."
		echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' > nadia_barcode.txt
		fi
		else
		#save original barcode file (if doesn't already exist)
		if [[ ! -f 737K-august-2016.txt.backup ]]; then
		echo " backing up whitelist of version 2 kit ..."
		cp 737K-august-2016.txt 737K-august-2016.txt.backup
		fi
		#combine 10x and Nadia barcodes
		cat nadia_barcode.txt 737K-august-2016.txt.backup \| sort \| uniq > 737K-august-2016.txt
		echo " whitelist converted for Nadia 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
		echo " restoring 10x barcodes for version 3 kit ..."
		cp 3M-february-2018.txt.backup.gz 3M-february-2018.txt.gz
		fi
		gunzip -k 3M-february-2018.txt.gz
		if [[ ! -f 3M-february-2018.txt.backup.gz ]]; then
		echo " backing up whitelist of version 3 kit ..."
		cp 3M-february-2018.txt 3M-february-2018.txt.backup
		gzip 3M-february-2018.txt.backup
		fi
		#combine 10x and Nadia barcodes
		if [[ ! -f nadia_barcode.txt.gz ]]; then
		gzip -f nadia_barcode.txt
		fi
		zcat nadia_barcode.txt.gz 3M-february-2018.txt.backup.gz \| sort \| uniq > 3M-february-2018.txt
		gzip -f 3M-february-2018.txt
		if [ -d translation ]; then
		rm translation/3M-february-2018.txt.gz
		ln -s ../3M-february-2018.txt.gz translation/3M-february-2018.txt.gz
		fi
		echo " whitelist converted for Nadia compatibility with version 3 kit"
		fi
		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		#disable functions if 10x technology run previously
		if [[ $lastcall == "10x" ]]; then
		sed -i "s/if gem_group == prev_gem_group/#if gem_group == prev_gem_group/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert barcode_idx >= prev_barcode_idx/#assert barcode_idx >= prev_barcode_idx/g" ${DIR}-cs/${VERSION}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/assert np.array_equal(in_mc.get_barcodes(), barcodes)/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${DIR}-cs/${VERSION}/lib/python/cellranger/molecule_counter.py
		fi
		echo " $DIR restored for $technology"

		#create a new version 2 barcode file
		if [[ $technology == "nadia" ]]; then
		#create a Nadia barcode file
		if [[ ! -f nadia_barcode.txt ]]; then
		if [[ -f nadia_barcide.txt.gz ]]; then
		gunzip nadia_barcode.txt.gz
		else
		echo " $DIR ready for $technology"
		echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' > nadia_barcode.txt
		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
		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)
		cat nadia_barcode.txt 737K-august-2016.txt.backup \| sort \| uniq > 737K-august-2016.txt
		elif [[ $technology == "icell8" ]]; then
		#create an iCell8 barcode file by copying from convert repo
		if [[ -f iCell8_barcode.txt.gz ]]; then
		rm iCell8_barcode.txt.gz
		fi
		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
		sed -i 's/^/AAAAA/g' iCell8_barcode.txt
		echo " imported expected barcodes for iCELL8 ..."
		fi
		echo "Valid barcodes can be calculated accurately for iCELL8"
		#save original barcode file (if doesn't already exist)
		if [[ ! -f 737K-august-2016.txt.backup ]]; then
		echo " backing up whitelist of version 2 kit ..."
		cp 737K-august-2016.txt 737K-august-2016.txt.backup
		rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt $barcodefolder/iCell8_barcode.txt
		sed -i 's/^/AAAAA/g' iCell8_barcode.txt #convert barcode whitelist to match converted barcodes
		cat iCell8_barcode.txt 737K-august-2016.txt.backup \| sort \| uniq > 737K-august-2016.txt
		else
		lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`
		lock=$(($lock-1))
		echo $lock > $lockfile
		echo "Error: technology ($technology) is not supported"
		cd -
		exit 1
		fi
		#replace 10x barcodes with icell8
		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
		echo " whitelist converted for $technology compatibility with version 2 kit."

		#create new 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
		@@ -771,18 +719,28 @@ if [[ $setup == "true" ]]; then
		cp 3M-february-2018.txt 3M-february-2018.txt.backup
		gzip 3M-february-2018.txt.backup
		fi
		#combine 10x and Nadia barcodes
		if [[ ! -f iCell8_barcode.txt.gz ]]; then

		#combine 10x and new barcodes
		if [[ $technology == "nadia" ]]; then
		if [[ ! -f nadia_barcode.txt.gz ]]; then
		gzip -f nadia_barcode.txt
		fi
		zcat nadia_barcode.txt.gz 3M-february-2018.txt.backup.gz \| sort \| uniq > 3M-february-2018.txt
		elif [[ $technology == "icell8" ]]; then
		if [[ -f iCell8_barcode.txt.gz ]]; then
		rm iCell8_barcode.txt.gz
		fi
		cat iCell8_barcode.txt > 3M-february-2018.txt
		fi
		gzip -f 3M-february-2018.txt

		if [ -d translation ]; then
		rm translation/3M-february-2018.txt.gz
		ln -s ../3M-february-2018.txt.gz translation/3M-february-2018.txt.gz
		fi
		echo " whitelist converted for iCELL8 compatibility with version 3 kit."
		fi
		echo " whitelist converted for $technology compatibility with version 3 kit."

		#if cellranger version is 3 or greater, restore assert functions
		if [[ `printf '%s\n' '$VERSION 3.0.0' \| sort -V \| head -n 1` != $VERSION ]]; then
		#disable functions if 10x technology run previously
		@@ -795,14 +753,8 @@ if [[ $setup == "true" ]]; then
		else
		echo " $DIR ready for $technology"
		fi
		else
		lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`
		lock=$(($lock-1))
		echo $lock > $lockfile
		echo "Error: technology ($technology) is not supported"
		cd -
		exit 1
		fi

		echo $technology > $lastcallfile
		cd -
		echo "setup complete"

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