Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert

    exit 1

fi

#check if ncores is an integer

ncores='^[0-9]+$'

if [[ -z "$ncells" ]]; then

int='^[0-9]+$'

if [[ -z "$ncores" ]]; then

    ncores=""

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

    echo "Error: option --localcores must be an integer"

#check if mem is a number

int='^[0-9]+([.][0-9]+)?$'

if [[ -z "$mem" ]]; then

    ncells=""

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

    mem=""

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

    echo "Error: option --localmem or --mempercore must be a number (of GB)"

    exit 1

fi

    echo "checking .lock file"

    lock=`cat $lockfile`

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

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

        echo " call accepted: no other cellranger jobs running"

        lock=1

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

             echo $lock > $lockfile

        fi

    else

        if [[ -f $lastcallfile ]]; then

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

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

                #add current job to lock

                lock=$(($lock+1))

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

                    echo $lock > $lockfile

                fi

                setup=false

            else

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

        echo $technology > $lastcallfile

    fi

    cd -

    exit 0

    echo "setup complete"

fi