Juicer tools rename

        echo "(-: Alignment and merge done, launching other jobs."

        $execstring

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/stats_dups.txt $outputdir/dups.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter.txt -q 1 $outputdir/merged_nodups.txt; cat $splitdir/*_abnorm.sam > $outputdir/abnormal.sam; cat $splitdir/*_unmapped.sam > $outputdir/unmapped.sam; awk -f ${juiceDir}/scripts/collisions.awk $outputdir/abnormal.sam > $outputdir/collisions.txt"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicebox pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" -w "done(${groupname}_stats)" -J "${groupname}_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicebox pre -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; else ${juiceDir}/scripts/juicer_tools pre -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 $outputdir/merged_nodups.txt $outputdir/inter.hic $genomePath; fi ;"

        bsub -o $topDir/lsf.out -q $long_queue -W $long_queue_time -R "rusage[mem=16000]" $waitstring22 -J "${groupname}_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; cat $splitdir/*.res.txt | awk -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter_30.txt; java -cp ${juiceDir}/scripts/ LibraryComplexity $outputdir inter_30.txt >> $outputdir/inter_30.txt; ${juiceDir}/scripts/statistics.pl -s $site_file -l $ligation -o $outputdir/inter_30.txt -q 30 $outputdir/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ -n \"$nofrag\" ]; then ${juiceDir}/scripts/juicer_tools pre -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; else ${juiceDir}/scripts/juicer_tools pre -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 $outputdir/merged_nodups.txt $outputdir/inter_30.hic $genomePath; fi"

DOSTAT

	waitstring3="#BSUB -w \" done(${groupname}_launch) \""

	waitstring4="-w \"done(${groupname}_hic30)\""