Commit 0ab06d24 authored by kai.b's avatar kai.b
Browse files

potentially a simpler version for --setup. see if this works Tom.

parent 90c00890

launch_universc.sh

+93 −188
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 0.2.0.900333) | head -n 3 | tail -n 2`

##########
@@ -82,8 +82,18 @@ fi 






#####reading in options#####

setup="false"

#####options#####

#set options

DIR=`which cellranger` #location of cellranger

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1` #get cellranger version

lockfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock #path for .lock file

lastcallfile=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called #path for .last_called

lastcall=`cat $lastcallfile`

barcodefolder=${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes #folder with the barcodes

cdrIN="input4cellranger" #name of the directory with all FASTQ files given to cellranger



#variable options

setup=false

read1=()

read2=()

SAMPLE=""
@@ -94,10 +104,7 @@ reference="" 
ncells=""

chemistry=""

jobmode=""

convert="keep"



DIR=`which cellranger`

VERSION=`cellranger count --version | head -n 2 | tail -n 1 | cut -d"(" -f2 | cut -d")" -f1`

convert=keep



next=false

for op in "$@"; do
@@ -163,8 +170,7 @@ for op in "$@"; do 
            ;;

        -f|--file)

            shift

            if [[ "$1" != "" ]]

                then

            if [[ "$1" != "" ]]; then

                arg=$1

                while [[ ! "$arg" == "-"* ]] && [[ "$arg" != "" ]]; do

                    read1+=("${1}_R1_001")
@@ -271,51 +277,6 @@ done 






#####check if UniverSC is running already#####

#create .lock file if none exists

if [[ ! -f  ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock ]]; then

    echo "creating lock file"

    echo 0 > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

fi



#check if jobs running (check value in .lock file)

echo "checking .lock file"

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`



if [[ ! $lock == "0" ]]; then

    echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR}"

    #check technology current running

    if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

        last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

        echo " running $lock jobs with technology $last"

        #check if the technology running is different from the current convert call

        if [[ $last == $technology ]]; then

            echo " no conflict detected"

            #add current job to lock

            echo " increment .lock"

            lock=$(($lock+1))

            echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

            echo " call accepted: running $lock cellranger jobs on $technology"

	else

	    echo "Error: conflict between technology selected for the new job ($technology) and for $lock jobs currently running ($last)"

            echo "barcode whitelist configured and locked for currently running technology: $last"

            echo "remove ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock if $last jobs have completed or aborted"

            exit 1

        fi

    fi

else

    #initialise lock file if first call (no other jobs running)

    #add disable increment for setup calls (which are not counted or removed)

    #add current job to lock

    echo " increment .lock"

    lock=$(($lock+1))

    echo " call accepted: running no other cellranger jobs"

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

fi

##########







#####check if input maches expected inputs#####

if [[ $verbose == "true" ]]; then

    echo "checking options ..."
@@ -323,33 +284,20 @@ fi 


#check if technology matches expected inputs

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option -t needs to be 10x, nadia, or icell8"

    exit 1

fi



#check if setup needs to be run before analysis

if [[ -z $setup ]]; then

    setup=false

fi



#check for presence of read1 and read2 files

if [[ ${#read1[@]} -eq 0 ]] && [[ $setup == "false" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

if [[ $setup == "false" ]]; then

    if [[ ${#read1[@]} -eq 0 ]]; then

        echo "Error: option -R1 or --file is required"

        exit 1

fi

if [[ ${#read2[@]} -eq 0 ]] && [[ $setup == "false" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    elif [[ ${#read2[@]} -eq 0 ]]; then

        echo "Error: option -R2 or --file is required"

        exit 1

    fi

fi



#check for file type (extension) for files

##allows incomplete file names and processing compressed files
@@ -365,7 +313,7 @@ for i in ${!read1[@]}; do 
            read=`echo $read | sed -e "s/\.gz//g"`

        fi

        if [[ $read != *"fastq" ]] && [[ $read != *"fq" ]]; then

            echo "***Warning: file $read is assubed to be in fastq format***"

            echo "***Warning: file $read is assumed to be in fastq format***"

        fi

        if [[ $verbose == "true" ]]; then

            echo "  $read"
@@ -383,9 +331,6 @@ for i in ${!read1[@]}; do 
            echo "  $read"

        fi

    else

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: $read not found"

        exit 1

    fi
@@ -422,9 +367,6 @@ for i in ${!read2[@]}; do 
            echo "  $read"

        fi

    else

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: $read not found"

        exit 1

    fi
@@ -435,6 +377,7 @@ done 
if [[ $verbose == "true" ]]; then

    echo " checking file name for $read1 ..."

fi



for i in ${!read1[@]}; do

    read=${read1[$i]}

    if [[ -h $read ]]; then
@@ -587,15 +530,9 @@ for fq in "${read1[@]}"; do 
    ln=`basename $fq | cut -f$(($name-1))  -d'_' | sed 's/L00//'`

    LANE+=($ln)

    if [[ $name < 4 ]]; then

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";

        exit 1

    elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: $fq does not have a .fq or .fastq extention"

        exit 1

    fi
@@ -604,9 +541,6 @@ for fq in "${read1[@]}"; do 
        if [[ -z $SAMPLE ]]; then

            SAMPLE=$sn

        else

            lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

            lock=$(($lock-1))

            echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

            echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."

            exit 1

        fi
@@ -619,15 +553,9 @@ for fq in "${read2[@]}"; do 
    LANE+=($ln)

    

    if [[ $name < 4 ]]; then

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: filename $fq is not following the naming convention. (e.g. EXAMPLE_S1_L001_R1_001.fastq)";

        exit 1

    elif [[ $fq != *'.fastq'* ]] && [[ $fq != *'.fq'* ]]; then

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: $fq does not have a .fq or .fastq extention"

        exit 1

    fi
@@ -636,9 +564,6 @@ for fq in "${read2[@]}"; do 
        if [[ -z $SAMPLE ]]; then

            SAMPLE=$sn

        else

            lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

            lock=$(($lock-1))

            echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

            echo "Error: some samples are labeled $SAMPLE while others are labeled $sn. cellranger can only handle files from one sample at a time."

            exit 1

        fi
@@ -648,15 +573,9 @@ LANE=$(echo "${LANE[@]}" | tr ' ' '\n' | sort -u | tr '\n' ',' | sed 's/,$//') 


#check if ID is present

if [[ -z $id ]] && [[ ${#read1[@]} -eq 0 ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option --id is required"

    exit 1

elif [[ $id == *" "* ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: \"$id\" for option -id must not contain a space"

    exit 1

fi
@@ -664,9 +583,6 @@ fi 
#check if reference is present

if [[ -z $reference ]]; then

    if [[ $setup == "false" ]] || [[ ${#read1[@]} -ne 0 ]] || [[ ${#read2[@]} -ne 0 ]]; then

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo "Error: option --reference is required";

        exit 1

    fi
@@ -677,9 +593,6 @@ int='^[0-9]+$' 
if [ -z "$ncells" ]; then

    ncells=""

elif ! [[ $ncells =~ $int ]] && [[ $setup == "false" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option --force-cells must be an integer"

    exit 1

fi
@@ -688,9 +601,6 @@ fi 
if [ -z "$chemistry" ]; then

    chemistry="SC3Pv2"

elif [[ "$chemistry" != "SC3Pv2" ]] && [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option --chemistry must be SC3Pv2, SC5P-PE , or SC5P-R2"

    exit 1

fi
@@ -699,21 +609,62 @@ fi 
if [ -z "$jobmode" ]; then

    jobmode="local"

elif [[ "$jobmode" != "local" ]] && [[ "$jobmode" != "sge" ]] && [[ "$jobmode" != "lsf" ]] && [[ "$jobmode" != *"template" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option --jobmode must be local, sge, lsf, or a .template file"

    exit 1

fi



#check if conversion matches expected input

if [[ "$convert" != "keep" ]] && [[ "$convert" != "skip" ]] && [[ "$convert" != "convert" ]]; then

    lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

    lock=$(($lock-1))

    echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    echo "Error: option --overwrite needs to be keep, skip, or convert"

    exit 1

fi



#check if setup needs to be run before analysis

if [[ -z $setup ]]; then

    setup=false

fi

if [[ $lastcall != $technology ]]; then

    setup=true

fi

##########







#####check if UniverSC is running already#####

#set up .lock file

if [[ ! -f $lockfile ]]; then

    echo "creating .lock file"

    echo 0 > $lockfile

else

    #check if jobs running (check value in .lock file)

    echo "checking .lock file"

    lock=`cat $lockfile`

    

    if [[ $lock -eq 0 ]]; then

        echo " call accepted: no other cellranger jobs running"

        lock=1

        echo $lock > $lockfile

    else

        if [[ -f $lastcallfile ]]; then

            echo " total of $lock cellranger ${VERSION} jobs already running in ${DIR} with technology $lastcall"

            

            #check if the technology running is different from the current convert call

            if [[ $lastcall == $technology ]]; then

                echo " call accepted: no conflict detected with other jobs currently running"

                #add current job to lock

                lock=$(($lock+1))

                echo $lock > $lockfile

	    else

	        echo "Error: conflict between technology selected for the new job ($technology) and other jobs currently running ($lastcall)"

                echo "barcode whitelist configured and locked for currently running technology: $lastcall"

                echo "remove $lockfile if $lastcall jobs have completed or aborted"

                exit 1

            fi

        else

            echo "Error: $lastcallfile not found"

        fi

    fi

fi

##########
@@ -722,17 +673,13 @@ fi 
echo ""

echo "#####Input information#####"

echo "SETUP: $setup"

if ! [[ $setup == "false" ]]; then

    echo "***Warning: whitelist is converted for compatibility, valid barcodes cannot be detected accurately with this technology***"

echo "FORMAT: $technology"

if [[ $technology == "nadia" ]]; then

    echo "***Warning: whitelist is converted for compatibility with $technology, valid barcodes cannot be detected accurately with this technology***"

fi

if [[ ${#read1[@]} -eq 0 ]] && [[ ${#read1[@]} -eq 0 ]]; then

    echo "***Warning: no FASTQ files were selected, launch_universc.sh will exit after setting up the whitelist***"

fi

fi

if ! [[ "$technology" == "10x" ]]; then

    echo "FORMAT: $technology"

else

    echo "FORMAT: $technology (no conversion)"

fi

if ! [[ ${#read1[@]} -eq 0 ]]; then

    echo "INPUT(R1):"

    for i in ${!read1[@]}; do
@@ -777,7 +724,7 @@ echo "" 
#run setup if called

if [[ $setup == "true" ]]; then

    echo "setup begin"

    if [[ ! -w ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes ]]; then

    if [[ ! -w $barcodefolder ]]; then

        echo "Error: launch_universc.sh can only be run cellranger installed locally"

        echo "Running cellranger installed at $DIR"

        echo "Install cellranger in a directory with write permissions such as /home/`whoami`/local"
@@ -786,13 +733,14 @@ if [[ $setup == "true" ]]; then 
        echo " `whereis cellranger`"

        exit 1

    fi

    cd ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes

    

    cd $barcodefolder

    

    if [[ -f 3M-february-2018.txt ]]; then

        gzip -f 3M-february-2018.txt

    fi

    

    echo "updating barcodes in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes for cellranger version $VERSION installed in $DIR ..."

    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)
@@ -815,8 +763,7 @@ if [[ $setup == "true" ]]; then 
        #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

            #restore functions if other technology run previously

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != $technology ]]; then

            if [[ $lastcall != $technology ]]; then

                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
@@ -845,7 +792,6 @@ if [[ $setup == "true" ]]; then 
            echo " backing up whitelist of version 2 kit ..."

            cp 737K-august-2016.txt 737K-august-2016.txt.backup

        fi

        echo "Warning: Valid barcodes cannot be calculated accurately for Nadia or DropSeq technology"

        #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."
@@ -873,8 +819,7 @@ if [[ $setup == "true" ]]; then 
        #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

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != "10x" ]]; then

            if [[ $lastcall != "10x" ]]; then

                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
@@ -935,8 +880,7 @@ if [[ $setup == "true" ]]; then 
        #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

            last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

            if [[ $last != "10x" ]]; then

            if [[ $lastcall != "10x" ]]; then

                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
@@ -947,12 +891,12 @@ if [[ $setup == "true" ]]; then 
    else

        lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

        lock=$(($lock-1))

        echo $lock > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

        echo $lock > $lockfile

        echo "Error: technology ($technology) is not supported"

        cd -

        exit 1

    fi

    echo $technology > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called

    echo $technology > $lastcallfile

    cd -

    echo "setup complete"

fi
@@ -968,37 +912,8 @@ fi 






#####detect whitelist directory#####

#check whitelist and run --setup if needed

echo "checking whitelist ..."

if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

    #run again if last technology called is different from technology

    last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

    if [[ $last != $technology ]]; then

        echo " running setup on $technology on whitelist in ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes ..."

        if [[ $verbose == "true" ]]; then

            echo " last: $last"

            echo " technology: $technology"

        fi

        bash $(basename "$0") -t $technology --setup

        setup=false

        if [[ $convert == "skip" ]]; then

            echo " ***Warning: technology changed to $technology since last run. FASTQ file conversion will be carreid out.***"

            convert="convert"

        fi

    fi

else    

    echo " using setup $technology from previous whitelist configuration ..."

    echo $technology > ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called

fi

echo "check complete"

##########







#####create directory with files fed to cellranger#####

echo "creating a folder for all cellranger input files ..."

crIN="input4cellranger"

convFiles=()



if [[ ! -d $crIN ]]; then
@@ -1143,26 +1058,17 @@ echo "" 
#####remove files if convert is not running elsewhere#####

echo "updating .lock file"



#reset lock counter (read in case changed by other jobs)

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`



#remove currewnt job from counter (successfully completed)

lock=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock`

lock=$(($lock-1))



#check if jobs running

if [[ $lock -ge 1 ]]; then

    echo " total of $lock cellranger ${VERSION} jobs still running in ${DIR}"

    #check technology current running

    if [[ -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called ]]; then

        last=`cat ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.last_called`

        echo " running technology $last with $lock jobs"

    fi

fi



#remove .lock file if no other jobs running exists (prevents negative values allowing technologies to run at same time)

if [[ $lock -le 0 ]]; then

    echo " no other jobs currently running: lock files cleared for cellranger ${VERSION} in ${DIR}"

    echo " total of $lock jobs for $lastcall technology are still run by cellranger ${VERSION} in ${DIR}"

else

    echo " no other jobs currently run by cellranger ${VERSION} in ${DIR}"

    echo " no conflicts: whitelist can now be changed for other technologies"

    rm -f ${DIR}-cs/${VERSION}/lib/python/cellranger/barcodes/.lock

    rm -f $lockfile

fi

##########
@@ -1182,4 +1088,3 @@ echo "$log" 
##########



exit 0

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