Update juicer.sh

        DpnII) ligation="GATCGATC";;

        MboI) ligation="GATCGATC";;

        NcoI) ligation="CCATGCATGG";;

        Arima) ligation="'(GAATAATC|GAATACTC|GAATAGTC|GAATATTC|GAATGATC|GACTAATC|GACTACTC|GACTAGTC|GACTATTC|GACTGATC|GAGTAATC|GAGTACTC|GAGTAGTC|GAGTATTC|GAGTGATC|GATCAATC|GATCACTC|GATCAGTC|GATCATTC|GATCGATC|GATTAATC|GATTACTC|GATTAGTC|GATTATTC|GATTGATC)'";;

        none) ligation="XXXX";;

        *)  ligation="XXXX"

            echo "$site not listed as recognized enzyme. Using $site_file as site file"

        fi

        touchfile=${tmpdir}/${jname}

        myjid=$(qsub -terse -o ${debugdir}/count_ligations-${groupname}-${jname}.out -e ${debugdir}/count_ligations-${groupname}-${jname}.err -q ${queue} -r y -l h_rt=${queue_time} -N ${groupname}${jname}countligations -v usegzip=${usegzip},name=${name},name1=${name1},name2=${name2},ext=${ext},ligation=${ligation} ${juiceDir}/scripts/countligations.sh)

        myjid=$(qsub -terse -o ${debugdir}/count_ligations-${groupname}-${jname}.out -e ${debugdir}/count_ligations-${groupname}-${jname}.err -q ${queue} -r y -l h_rt=${queue_time} -N ${groupname}${jname}countligations -v usegzip=${usegzip},name=${name},name1=${name1},name2=${name2},ext=${ext},ligation="${ligation}" ${juiceDir}/scripts/countligations.sh)

        echo "Count ligations $jname job $myjid" >> ${debugdir}/jobs-${groupname}.out

        if [ -z $chimeric ] 

        then