add lock file to cellranger barcode directory to prevent changing whitelist while running

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

fi

#import lock counter

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

#check if jobs running

if [[ $lock -ge 1 ]]

    then

    echo "$lock number of cellranger ${VERSION} jobs 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"

        #check if currently running technology is different to convert call

        if [[ $last == $technology ]]

           then

           echo "no conflict detected"

           #add current job to lock

           lock=$(($lock+1))

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

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

        else

           echo "conflict between $technology and current $lock cellranger runs on $last"

           echo "***Please hold calls for $technology until jobs running $last are completed"

           stop "***Error: barcode whitelist configured for currently running technology: $last" 

        fi

    fi

fi

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 "$(($lock+1))"

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

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