Remove internal SLURM option (d761949e) · Commits · github_fork / ZUMIs

zUMIs-config_shiny.R

+44 −47

Original line number	Diff line number	Diff line
		@@ -77,7 +77,6 @@ ui <- fluidPage(
		numericInput("numThreads","Number of CPU Threads:",value=8,min=1,step=1),
		numericInput("memLimit","Memory limit (Gb) 0 = no limit:",value=0,step=1),
		checkboxInput("makeStats",label="Produce summary statistics",value = T),
		checkboxInput("useSLURM",label="Use SLURM workload manager",value = F),
		selectInput("whichStage",label = "Start zUMIs from following stage:",choices = c("Filtering", "Mapping", "Counting", "Summarising"),selected = "Filtering",multiple = F)
		)),

		@@ -271,7 +270,6 @@ server <- function(input, output, session) {
		"twoPass" = input$twoPass
		),
		"make_stats" = input$makeStats,
		"use_SLURM" = input$useSLURM,
		"which_Stage" = input$whichStage
		)
		return(y)
		@@ -332,7 +330,6 @@ server <- function(input, output, session) {
		updateNumericInput(session = session, inputId = "numThreads", value = ya$num_threads)
		updateNumericInput(session = session, inputId = "memLimit", value = ya$mem_limit)
		updateCheckboxInput(session = session, inputId = "makeStats", value = ya$make_stats)
		updateCheckboxInput(session = session, inputId = "useSLURM", value = ya$use_SLURM)
		updateSelectInput(session = session, inputId = "whichStage", selected = ya$which_Stage)
		updateCheckboxInput(session = session, inputId = "countIntrons", value = ya$counting_opts$introns)
		updateTextInput(session = session, inputId = "downsamp", value = ya$counting_opts$downsampling)

zUMIs-master.sh

+1 −45

Original line number	Diff line number	Diff line
		@@ -79,7 +79,6 @@ num_threads=`grep 'num_threads' $yaml \| awk '{print $2}'`
		project=`grep 'project:' $yaml \| awk '{print $2}'`
		whichStage=`grep 'which_Stage:' $yaml \| awk '{print $2}'`
		outdir=`grep 'out_dir' $yaml \| awk '{print $2}'`
		isslurm=`grep 'use_SLURM:' $yaml \| awk '{print $2}'`
		genomedir=`grep 'STAR_index:' $yaml \| awk '{print $2}'`
		mem_limit=`grep 'mem_limit:' $yaml \| awk '{print $2}'`
		isstats=`grep 'make_stats:' $yaml \| awk '{print $2}'`
		@@ -140,27 +139,6 @@ then

		tmpMerge=$outdir/zUMIs_output/.tmpMerge/

		if [[ "$isslurm" == "yes" ]]; then

		if [[ $f =~ \.gz$ ]]; then

		for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f" >> $outdir/$project.slurmjobid.txt;done
		else
		for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f" >> $outdir/$project.slurmjobid.txt;done
		fi

		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`

		sbatch --cpus-per-task=1 --job-name=listPrefix --dependency=afterok:$j --mem=1M --wrap="bash $zumisdir/listPrefix.sh $zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc" >> $outdir/$project.slurmjobid.txt

		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`

		sbatch --cpus-per-task=1 --job-name=mergeBAM --dependency=afterok:$j --mem=1M --wrap="bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml" >> $outdir/$project.slurmjobid.txt

		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`

		else

		if [[ $f =~ \.gz$ ]]; then
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f & done
		wait
		@@ -177,21 +155,14 @@ then
		wait
		bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml
		fi
		fi

		if
		[[ "$whichStage" == "Filtering" ]] \|\|
		[[ "$whichStage" == "Mapping" ]]
		then
		echo "Mapping..."
		if [[ "$isslurm" == "yes" ]]; then
		memory=`du -sh $genomedir \| cut -f1` #STAR genome index size
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		sbatch --dependency=afterok:$j --job-name=mapping --mem=$memory --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-mapping.R $yaml" >> $outdir/$project.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-mapping.R $yaml
		fi
		fi

		if
		[[ "$whichStage" == "Filtering" ]] \|\|
		@@ -200,18 +171,8 @@ if
		then
		echo "Counting..."
		yamlnew=$outdir/$project.postmap.yaml #note! mapping creates a temporary new yaml because of custom GTF!
		if [[ "$isslurm" == "yes" ]]; then
		if [[ $mem_limit == "null" ]]; then
		mem_limit=`du -sh $genomedir \| cut -f1`
		else
		mem_limit=`expr $mem_limit \* 1000`
		fi
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		sbatch --dependency=afterok:$j --mem=$mem_limit --job-name=dge --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-dge2.R $yamlnew" >> $outdir/$project.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-dge2.R $yamlnew
		fi
		fi

		if
		[[ "$whichStage" == "Filtering" ]] \|\|
		@@ -222,11 +183,6 @@ then
		yamlnew=$outdir/$project.postmap.yaml #note! mapping creates a temporary new yaml because of custom GTF!
		if [[ "$isstats" == "yes" ]]; then
		echo "Descriptive statistics..."
		if [[ "$isslurm" == "yes" ]]; then
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		sbatch --dependency=afterok:$j --mem=5000 --job-name=stats --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" >> $outdir/$project.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-stats2.R $yamlnew
		fi
		fi
		fi

zUMIs.yaml

+0 −2

Original line number	Diff line number	Diff line
		@@ -75,8 +75,6 @@ counting_opts:
		#produce stats files and plots?
		make_stats: yes

		#use SLURM workload manger?
		use_SLURM: no

		#Start zUMIs from stage. Possible TEXT(Filtering, Mapping, Counting, Summarising). Default: Filtering.
		which_Stage: Filtering

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