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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
###########  The main control script, that we will run and can be run seperately later if the job fails at intermediate stages  ###################
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RUNVAR1=""$HASHBANG"

echo Killing any running jobs in "$OUTPUTDIR"
trinity_kill.pl "$OUTPUTDIR" 2> /dev/null >/dev/null
echo Checking and submitting any jobs
###########################################################################################################################################################
################         Use the Trinity/Chrysalis checkpoint files to work out what part of job remains          #########################################
################         and queue only those parts that are still required		                                  #########################################

if [ -s \""$OUTPUTDIR"/Trinity.fasta\" ] ; then 
	echo 'Trinity seemingly finished: Trinity.fasta present in output directory. If you think this is wrong, delete Trinity.fasta and re-submit'
	exit 0
fi


if [ ! -e \""$OUTPUTDIR"/inchworm.K25.L25"$DS"fa.finished\" ] ;then # do the whole analysis 
	PBS_JOB1=\`qsub  "$JOBNAME1".sh\`
	PBS_JOB2=\`qsub -W depend=afterok:\$PBS_JOB1  "$JOBNAME2".sh\`
	PBS_JOB3=\`qsub -W depend=afternotok:\$PBS_JOB2 "$JOBNAME3".sh\`
	PBS_JOB4_2=\`qsub -W depend=afterok:\$PBS_JOB2,afterany:\$PBS_JOB3 "$JOBNAME4".sh\`
	echo  "$JOBNAME1".sh submitted ; echo \"\$PBS_JOB1\" > jobnumbers.out ;
	echo  "$JOBNAME2".sh submitted ; echo \"\$PBS_JOB2\" >> jobnumbers.out ;
	echo  "$JOBNAME3".sh submitted ; echo \"\$PBS_JOB3\" >> jobnumbers.out ;
	echo  "$JOBNAME4".sh post-job "$JOBNAME2" submitted ; echo \"\$PBS_JOB4_2\" >> jobnumbers.out ;
else # do analysis after inchworm only
	if [ ! -e \""$OUTPUTDIR"/chrysalis/GraphFromIwormFasta.finished\" ] ; 	then # start analysis after inchworm 
		PBS_JOB2=\`qsub  "$JOBNAME2".sh\`
		PBS_JOB3=\`qsub -W depend=afternotok:\$PBS_JOB2 "$JOBNAME3".sh\`
		PBS_JOB4_2=\`qsub -W depend=afterok:\$PBS_JOB2,afterany:\$PBS_JOB3 "$JOBNAME4".sh\`
		echo  "$JOBNAME2".sh submitted ; echo \"\$PBS_JOB2\" >  jobnumbers.out ;
		echo  "$JOBNAME3".sh submitted ; echo \"\$PBS_JOB3\" >> jobnumbers.out ;
		echo  "$JOBNAME4".sh post-job "$JOBNAME2" submitted ; echo \"\$PBS_JOB4_2\" >> jobnumbers.out ;
	else 
		if [ ! -e \""$OUTPUTDIR"/chrysalis/readsToComponents.finished\" ] ;then # start analysis at Chrisyalis ReadsToTranscripts - which is slow due to I/O 
			PBS_JOB3=\`qsub  "$JOBNAME3".sh\`
			PBS_JOB4=\`qsub -W depend=afterok:\$PBS_JOB3  "$JOBNAME4".sh\`
			echo  "$JOBNAME3".sh submitted ; echo \"\$PBS_JOB3\" >  jobnumbers.out ;
			echo  "$JOBNAME4".sh post-job "$JOBNAME3" submitted ; echo \"\$PBS_JOB4\" >> jobnumbers.out ;
		else # Run Chrysalis QuantifyGraph and then Butterfly 
			PBS_JOB4=\`qsub "$JOBNAME4".sh\`
			echo  "$JOBNAME4".sh submitted ; echo \"\$PBS_JOB4\"  > jobnumbers.out ;
		fi	
	fi		
	echo When JOB ID \"\$PBS_JOB4\" finishes successfully - see output: \"$OUTPUTDIR\"/\"$JOBNAME4\".o\"\$PBS_JOB4\" - either re-run the submit command or use the following command to get all the data into a single file:
	echo ' find "$OUTPUTDIR"/chrysalis -name *allProbPaths.fasta -exec cat {} \\; > "$OUTPUTDIR"/Trinity.fasta '
fi
" 	

echo "${RUNVAR1}" | cat -> ""$JOBPREFIX"_run.sh"
chmod 744 ""$JOBPREFIX"_run.sh"
echo "To restart these jobs run either the same command again:"
echo "    trinity_pbs.sh <the same .config file> "
echo "	or the following script: "
echo "    "$JOBPREFIX"_run.sh  found in the output directory "$OUTPUTDIR" "
echo "To stop these jobs run:"
echo "    trinity_kill.pl "$OUTPUTDIR" "
echo "To check progress of these jobs run:"
echo "    qstat -u "$USER""
echo ""