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##########################     Trinity PBS job submission with multi part dependencies    ########################################
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### Author: Josh Bowden, Alexie Papanicolaou, CSIRO
### Version 1.0
### QuantifyGraph and Butterfly p4a Script
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# we will not use array in order to ensure only jobs that have not finished are Submitting.
# this does cause a problem when wanting to kill them manually but best to use kill script
## JOBPREFIX is passed via HASHBANG
JOBSTRING4=""$HASHBANG"
"$NODESCPUS"
 JOB_CHRYSALIS="$JOBPREFIX"_p4b
 JOB_BUTTERFLY="$JOBPREFIX"_p5b
 cd "$OUTPUTDIR"

 rm -f \$JOB_CHRYSALIS.jobnames \$JOB_BUTTERFLY.jobnames
 FILENAME=""$OUTPUTDIR"/chrysalis/quantifyGraph_commands"
 FILENAMEBFLY=""$OUTPUTDIR"/chrysalis/butterfly_commands"

 if [ ! -e \$FILENAME.pbs ];then
	sed  -e 's/.*/if [[ -e SEDPLACEHOLDER ]]; then &;fi/' \$FILENAME|sed -r 's/(-e\s)SEDPLACEHOLDER(\s.+-i\s)(\S+).tmp/\1\3.tmp\2\3.tmp/' > \$FILENAME.pbs
	split -d -a 3 -l "1000" \$FILENAME.pbs  \$FILENAME.pbs.  
	sleep 5
 fi
 if [ ! -e \$FILENAMEBFLY.pbs ];then
	sed  -e 's/.*/if [ -e SEDPLACEHOLDER ]; then &;fi/' \$FILENAMEBFLY|sed -r 's/(-e\s)SEDPLACEHOLDER(\s.+-C\s)(\S+)/\1\3.out\2\3/' > \$FILENAMEBFLY.pbs
	split -d -a 3 -l "1000" \$FILENAMEBFLY.pbs  \$FILENAMEBFLY.pbs. 
	sleep 5
 fi

 FILENAME=\$FILENAME.pbs
 FILENAMEBFLY=\$FILENAMEBFLY.pbs

 NUMCMDS=\`ls -l \$FILENAME.??? | wc -l\`
 NUMCMDSBFLY=\`ls -l \$FILENAMEBFLY.??? | wc -l\`
 let NUMCMDS=\$NUMCMDS-1
 let NUMCMDSBFLY=\$NUMCMDSBFLY-1
 let SUBMITTED_C=0
 let SUBMITTED_B=0

 for ((JOBID=0;JOBID<=\$NUMCMDS;++JOBID));do
  JOB_INDEX_PADDED=\`printf "%03d" \$JOBID\`
  MYJOBQ=\""\$FILENAME".\$JOB_INDEX_PADDED\"
  MYJOBB=\""\$FILENAMEBFLY".\$JOB_INDEX_PADDED\"
  JOB_FILESIZE_Q=\$(stat -c%s \$MYJOBQ)
  JOB_FILESIZE_B=\$(stat -c%s \$MYJOBB)

  #if some Q have completed:
  if [ -s  \"\$MYJOBQ.completed\" ] ; then
        JOB_COMPLETED_FILESIZE_Q=\$(stat -c%s \"\$MYJOBQ.completed\")
        # if not all have completed then run both Q and B
        if [ \"\$JOB_FILESIZE_Q\" -gt \"\$JOB_COMPLETED_FILESIZE_Q\" ] ; then
                PBS_JOB4=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_CHRYSALIS.sh\" \`
		if [[ ! \$PBS_JOB4 ]]; then
			echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_CHRYSALIS.sh\" FAILED. Aborting...\"
			exit 255
		fi
		let SUBMITTED_C++
                echo \$PBS_JOB4 >> \"\$JOB_CHRYSALIS.jobnames\"
                echo \$PBS_JOB4 >> jobnumbers.out ;
                PBS_JOB5=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED -W depend=afterok:$PBS_JOB4 \"\$JOB_BUTTERFLY.sh\" \`
		if [[ ! \$PBS_JOB5 ]]; then
			echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED -W depend=afterok:$PBS_JOB4 \"\$JOB_BUTTERFLY.sh\" FAILED. Aborting...\"
			exit 255
		fi
		let SUBMITTED_B++
                echo \$PBS_JOB5 >> \"\$JOB_BUTTERFLY.jobnames\"
                echo \$PBS_JOB5 >> jobnumbers.out ;
		if [ \$(( \$JOBID % 20 )) -eq 0 ] ; then
			echo Submitting up to 20 Quantify and/or Butterfly jobs
			sleep 3 # be nice
		fi
        # else all Q have completed; have B completed?
        else
                # if at least some B have completed
                if [ -s \"\$MYJOBB.completed\" ] ; then
                        JOB_COMPLETED_FILESIZE_B=\$(stat -c%s \"\$MYJOBB.completed\" )
                        # if not all, run them with no dependency (Q has completed)
                        if [ \"\$JOB_FILESIZE_B\" -gt \"\$JOB_COMPLETED_FILESIZE_B\" ] ; then
                                PBS_JOB5=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_BUTTERFLY.sh\" \`
				if [[ ! \$PBS_JOB5 ]]; then
					echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_BUTTERFLY.sh\" FAILED. Aborting...\"
					exit 255
				fi
				let SUBMITTED_B++
                                echo \$PBS_JOB5 >> \"\$JOB_BUTTERFLY.jobnames\"
                                echo \$PBS_JOB5 >> jobnumbers.out ;
				if [ \$(( \$JOBID % 20 )) -eq 0 ] ; then
					echo Submitting up to 20 Quantify and/or Butterfly jobs
					sleep 3 # be nice
				fi
                        fi
                # else no Q have completed; run them without dependency
                else
                        PBS_JOB5=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_BUTTERFLY.sh\" \`
			if [[ ! \$PBS_JOB5 ]]; then
				echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_BUTTERFLY.sh\" FAILED. Aborting...\"
				exit 255
			fi
			let SUBMITTED_B++
                        echo \$PBS_JOB5 >> \"\$JOB_BUTTERFLY.jobnames\"
                        echo \$PBS_JOB5 >> jobnumbers.out ;
			if [ \$(( \$JOBID % 20 )) -eq 0 ] ; then
				echo Submitting up to 20 Quantify and/or Butterfly jobs
				sleep 3 # be nice
			fi
                fi
        fi
 # neither Q (and thus nor B) have ever ran successfully, submit both with a dependency
 else
        PBS_JOB4=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_CHRYSALIS.sh\" \`
	if [[ ! \$PBS_JOB4 ]]; then
		echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED \"\$JOB_CHRYSALIS.sh\" FAILED. Aborting...\"
		exit 255
	fi
	let SUBMITTED_C++
        echo \$PBS_JOB4 >> \"\$JOB_CHRYSALIS.jobnames\"
        echo \$PBS_JOB4 >> jobnumbers.out ;
        PBS_JOB5=\`qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED -W depend=afterok:\$PBS_JOB4 \"\$JOB_BUTTERFLY.sh\" \`
	if [[ ! \$PBS_JOB5 ]]; then
           echo \"Submission for qsub -v JOB_INDEX_PADDED=\$JOB_INDEX_PADDED -W depend=afterok:\$PBS_JOB4 \"\$JOB_BUTTERFLY.sh\" FAILED. Aborting...\"
           exit 255
        fi
	let SUBMITTED_B++
        echo \$PBS_JOB5 >> \"\$JOB_BUTTERFLY.jobnames\"
        echo \$PBS_JOB5 >> jobnumbers.out ;
	if [ \$(( \$JOBID % 20 )) -eq 0 ] ; then
		echo Submitting up to 20 Quantify and/or Butterfly jobs
		sleep 3 # be nice
	fi
 fi
 done
 
 echo Submitted \$SUBMITTED_C Chrysalis and \$SUBMITTED_B Butterfly jobs

 if [[ \$SUBMITTED_B == 0 && \$SUBMITTED_C == 0 ]]; then
 	echo \"No Trinity jobs need to be submitted \"
	if [ -s "$OUTPUTDIR"/Trinity.fasta.complete ]; then
		echo \"Trinity RNA-Seq assembly is complete! Result file is present as "$OUTPUTDIR"/Trinity.fasta \"
	else
		echo \"Proceeding with capturing the output with this command\"
        	echo ' find "$OUTPUTDIR"/chrysalis -name *allProbPaths.fasta -exec cat {} \\; > "$OUTPUTDIR"/Trinity.fasta '
		find "$OUTPUTDIR"/chrysalis -name *allProbPaths.fasta -exec cat {} \\; > "$OUTPUTDIR"/Trinity.fasta
		touch "$OUTPUTDIR"/Trinity.fasta.complete
                echo DO: rm -f "$OUTPUTDIR"/bowtie.nameSorted.sam* "$OUTPUTDIR"/both.fa* "$OUTPUTDIR"/inchworm.kmer_count "$OUTPUTDIR"/iworm_* "$OUTPUTDIR"/target* "$OUTPUTDIR"/jellyfish* "$OUTPUTDIR"/scaffolding* "$OUTPUTDIR"/*.finished "$OUTPUTDIR"/mer_counts_* 
	fi
 fi
"


######
##### Write the above script to a file for later execution
echo "${JOBSTRING4}" | cat -> "$JOBNAME4.sh"