#!/bin/sh ## Usage # sh step5-derfinderReport.sh brainspan run5-v1.5.30 # Define variables EXPERIMENT=$1 SHORT="derR-${EXPERIMENT}" PREFIX=$2 # Directories ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derSupplement MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/derAnalysis # Construct shell files outdir="${PREFIX}" sname="${SHORT}.${PREFIX}" echo "Creating script ${sname}" cat > ${ROOTDIR}/.${sname}.sh <<EOF #!/bin/bash #$ -cwd #$ -m e #$ -l mem_free=150G,h_vmem=180G,h_fsize=20G #$ -N ${sname} #$ -hold_jid derM-${EXPERIMENT}.${PREFIX} echo "**** Job starts ****" date mkdir -p ${WDIR}/${outdir}/logs # merge results cd ${WDIR} module load R/3.3 Rscript -e "library(regionReport); load('${MAINDIR}/CoverageInfo/fullCov.Rdata'); derfinderReport(prefix='${PREFIX}', browse=FALSE, nBestRegions = 100, nBestClusters=20, fullCov=fullCov, device='CairoPNG', clean = FALSE, significantVar='fwer'); Sys.time(); proc.time(); options(width = 120); devtools::session_info()" # Move log files into the logs directory mv ${ROOTDIR}/${sname}.* ${WDIR}/${outdir}/logs/ echo "**** Job ends ****" date EOF call="qsub .${sname}.sh" echo $call $call