#!/bin/sh ## Usage # sh step1-fullCoverage.sh brainspan # Define variables EXPERIMENT=$1 SHORT="fullCov-${EXPERIMENT}" CORES=10 # Directories ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derSupplement MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/CoverageInfo if [[ "${EXPERIMENT}" == "brainspan" ]] then DATADIR=/nexsan2/disk3/ajaffe/BrainSpan/RNAseq/bigwig/ CUTOFF=0.25 else echo "Specify a valid experiment: brainspan" fi # Construct shell file echo 'Creating script for loading the Coverage data' cat > ${ROOTDIR}/.${SHORT}.sh <<EOF #!/bin/bash #$ -cwd #$ -m e #$ -l mem_free=20G,h_vmem=30G,h_fsize=40G #$ -N ${SHORT} #$ -pe local ${CORES} echo '**** Job starts ****' date # Make logs directory mkdir -p ${WDIR}/logs # Load the data, save the coverage without filtering, then save each file separately cd ${WDIR} module load R/3.3 module load samtools/1.1 Rscript ${ROOTDIR}/step1-fullCoverage.R -d "${DATADIR}" -p "out$" -c "${CUTOFF}" -m ${CORES} ## Move log files into the logs directory mv ${ROOTDIR}/${SHORT}.* ${WDIR}/logs/ echo '**** Job ends ****' date EOF call="qsub .${SHORT}.sh" echo $call $call