Commit 688fc4f3 authored by mzhibo's avatar mzhibo Committed by GitHub
Browse files

Add files via upload 

1.fixed some bugs caused bye the $EMAIL variable. Now email notification of job errors covers all jobs in the main juicer.sh script. Add manually if you also want it in launch_stats.sh and postprocessing.sh. I could not pass this EMAIL="#PBS -M xxx@xxx.xx" value to these two scripts due to inexperience in coding...
2.deleted $resolutions I personally added in juicer.sh for my own project. This could potentially cause problems when it's not set. Without this, it will just run the default resolutions.
parent b8cecf01

PBS/scripts/juicer.sh

0 → 100644
+1118 −0

File added.

Preview size limit exceeded, changes collapsed.

PBS/scripts/launch_stats.sh

0 → 100644
+179 −0
Changes for PBS/scripts/launch_stats.sh: 179 added lines, 0 removed lines.
Original line number Diff line number Diff line 
#!/bin/bash

echo "check the variables:"

echo "${juiceDir}/scripts/launch_stats.sh"

echo "genomename: $groupname"

echo "juiceDir: $juiceDir"

echo "about: $about"

echo "site_file: $site_file"

echo "logdir: ${logdir}"

echo "ligation: $ligation"

echo "outputdir: $outputdir"

echo "splitdir: $splitdir"

echo "nofrag: $nofrag"

echo "final: $final"

echo "genomePath: $genomePath"

echo "queue $queue"

echo "resolutions: $resolutions"

echo "walltime: $walltime"

echo "long_walltime: $long_walltime"

echo $load_java

jID_osplit=$( qstat | grep osplit${groupname} | cut -c 1-7 )



if [ -z $final ]

then

	 waitstring2="#PBS -W depend=afterok:${jID_osplit}"

fi



echo "jID_osplit: $jID_osplit"

echo "waitstring2 is"

echo $waitstring2

timestamp=$(date +"%s" | cut -c 4-10)

qsub <<DOSTAT

#PBS -S /bin/bash

#PBS -q batch

#PBS -l nodes=1:ppn=1:AMD

#PBS -l mem=1gb

#PBS -l $walltime

#PBS -o ${logdir}/${timestamp}_launch_${groupname}.log

#PBS -j oe

#PBS -N Lnch_${groupname}

${waitstring2}



date +"%Y-%m-%d %H:%M:%S"

echo "Alignment and merge done, launching the stats job"

#jID_osplit=\$( qstat | grep osplit${groupname} | cut -c 1-7 )

jID_rmsplit=\$( qstat | grep RmSplt${groupname} | cut -c 1-7)



if [ -z $final ]

then

    waitstring22="#PBS -W depend=afterok:\${jID_rmsplit}"

fi

echo "waitstring22 is below"

echo ${waitstring22}

echo "jID_rmsplit value is: \${jID_rmsplit}"

echo "this is the value of waitstring22: \${waitstring22}"

timestamp=\$(date +"%s" | cut -c 4-10)

echo "start sbumitting stats job"

qsub <<STATS0

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=20gb

	#PBS -l $walltime

	\${waitstring22}

	#PBS -o ${logdir}/\${timestamp}_stats0_${groupname}.log

	#PBS -j oe

	#PBS -N stats0${groupname}



	date +"%Y-%m-%d %H:%M:%S"

	$load_java

	export _JAVA_OPTIONS=-Xmx16384m; 

	export LC_ALL=en_US.UTF-8



	tail -n1 $headfile | awk '{printf"%-1000s\n", \\\$0}' > $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



STATS0



qsub <<STATS30

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=20gb

	#PBS -l $walltime

	#PBS -o ${logdir}/\${timestamp}_stats_${groupname}.log

	#PBS -j oe

	#PBS -N stats30${groupname}

	\${waitstring22}

	

	date +"%Y-%m-%d %H:%M:%S"

	$load_java

	export _JAVA_OPTIONS=-Xmx16384m; 

	export LC_ALL=en_US.UTF-8

	echo -e 'Experiment description: $about' > $outputdir/inter_30.txt; 

	tail -n1 $headfile | awk '{printf"%-1000s\n", \\\$0}' > $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



STATS30





qsub <<- ABNORMAL

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -o ${logdir}/\${timestamp}_abnormal_${groupname}.log

	#PBS -j oe

	#PBS -N abnorm_${groupname}

	\$waitstring22

	

	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

ABNORMAL



jID_stats0=\$( qstat | grep stats0${groupname} | cut -c 1-7)



wait

echo "this is the value of jID_stats: \${jID_stats}"

timestamp=\$(date +"%s" | cut -c 4-10)

echo "start submitting hic job"

qsub <<- HICWORK

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -o ${logdir}/\${timestamp}_hic0_${groupname}.log

	#PBS -j oe

	#PBS -N hic0_${groupname}

	#PBS -W depend=afterok:\${jID_stats0}

	

	date +"%Y-%m-%d %H:%M:%S"

	echo "finished stats job,now launching the hic job."    

	${load_java}

	export _JAVA_OPTIONS=-Xmx16384m

	if [ \"$nofrag\" -eq 1 ]

	then 

		${juiceDir}/scripts/juicer_tools 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

HICWORK

jID_stats30=\$( qstat | grep stats30${groupname} | cut -c 1-7)

timestamp=\$(date +"%s" | cut -c 4-10)

echo "start submitting hic30 job"

qsub <<- HIC30WORK

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l nodes=1:ppn=1:AMD

	#PBS -l mem=60gb

	#PBS -l $long_walltime

	#PBS -o ${logdir}/\${timestamp}_hic30_${groupname}.log

	#PBS -j oe

	#PBS -N hic30_${groupname}

	#PBS -W depend=afterok:\${jID_stats30}

	

	date +"%Y-%m-%d %H:%M:%S"

	$load_java

	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

	if [  \"$nofrag\" -eq 1 ]

	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

HIC30WORK



DOSTAT

PBS/scripts/postprocessing.sh

0 → 100644
+98 −0
Changes for PBS/scripts/postprocessing.sh: 98 added lines, 0 removed lines.
Original line number Diff line number Diff line 
#!/bin/bash

jID_launch=$( qstat | grep Lnch_${groupname} | cut -c 1-7 )

if [ -z $postproc ]

then

    waitstring3="#PBS -W depend=afterok:${jID_launch}"

fi

echo "waitstring3 is: ${waitstring3}"



timestamp=$(date +"%s" | cut -c 4-10)

qsub <<- POSTPROCWRAP

#PBS -S /bin/bash

#PBS -q $queue

#PBS -l $walltime

#PBS -l nodes=1:ppn=1:AMD

#PBS -l mem=4gb

#PBS -o ${logdir}/${timestamp}_postproc_wrap_${groupname}.log

#PBS -j oe

#PBS -N PPrWrp${groupname}

${waitstring3}



date +"%Y-%m-%d %H:%M:%S"



jID_hic30=\$(qstat | grep hic30_${groupname} |cut -c 1-7)



if [ -z $postproc ]

then

    waitstring4="#PBS -W depend=afterok:\${jID_hic30}" 

fi

echo "waitstring4 is : ${waitstring4}"



timestamp=\$(date +"%s" | cut -c 4-10)

qsub <<POSTPROCESS

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l $long_walltime

	#PBS -l nodes=1:ppn=1:gpus=1:GPU 

	#PBS -l mem=60gb

	#PBS -o ${logdir}/\${timestamp}_postproc_${groupname}.log

	#PBS -j oe

	#PBS -N PProc_${groupname}

    $waitstring4



    date +"%Y-%m-%d %H:%M:%S"

    $load_java

    $load_cuda

    module list 

    export _JAVA_OPTIONS=-Xmx16384m

    export LC_ALL=en_US.UTF-8



    ${juiceDir}/scripts/juicer_postprocessing.sh -j ${juiceDir}/scripts/juicer_tools -i ${outputdir}/inter_30.hic -m ${juiceDir}/references/motif -g $genomeID



POSTPROCESS

POSTPROCWRAP



jID_postprocwrap=$( qstat |grep PPrWrp${groupname} | cut -c 1-7 )

echo $jID_postprowrap

wait

timestamp=$(date +"%s" | cut -c 4-10)

qsub <<- FINCK

#PBS -S /bin/bash

#PBS -q $queue  

#PBS -l $walltime

#PBS -o ${logdir}/${timestamp}_prep_done_${groupname}.log

#PBS -j oe

#PBS -N Pdone_${groupname}

#PBS -W depend=afterok:${jID_postprocwrap}



date +"%Y-%m-%d %H:%M:%S"    

jID_hic30=\$(qstat | grep hic30_${groupname} |cut -c 1-7)

jID_stats0=\$(qstat | grep stats0${groupname} |cut -c 1-7)

jID_stats30=\$(qstat | grep stats30${groupname} |cut -c 1-7)

jID_hic=\$(qstat | grep hic0_${groupname} |cut -c 1-7)

jID_postproc=\$(qstat | grep PProc_${groupname} |cut -c 1-7)



waitstring5="#PBS -W depend=afterok:\${jID_postproc}"

if [ -z $postproc ]

then

    waitstring5="#PBS -W depend=afterok:\${jID_hic30}:\${jID_stats0}:\${jID_stats30}:\${jID_hic}:\${jID_postproc}"

fi

timestamp=\$(date +"%s" | cut -c 4-10)

qsub <<DONE

	#PBS -S /bin/bash

	#PBS -q $queue

	#PBS -l $walltime

	#PBS -l nodes=1:ppn=1:AMD 

	#PBS -l mem=4gb

	#PBS -o ${logdir}/\${timestamp}_done_${groupname}.log

	#PBS -j oe

	#PBS -N done_${groupname}

	\${waitstring5}



	date +"%Y-%m-%d %H:%M:%S"    

	export splitdir=${splitdir}

	export outputdir=${outputdir}

	${juiceDir}/scripts/check.sh

DONE

FINCK

CRA Git | Maintained and supported by SUSTech CRA and CCSE