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run.sh
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run.sh
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#!/bin/bash
#SDIR="$( cd "$( dirname "$0" )" && pwd )"
# HAL Location
export SDIR="/cbio/ski/chan/home/riazn/programs/FACETS.app"
# saba location
if [ ! -e $SDIR ]; then
export SDIR="/home/riazn/programs/FACETS.app"
fi
if [ "$#" -ne "2" ]; then
echo
echo "Too few arguments"
echo
echo " usage:: FACETS/App.sh NORMALBAM TUMORBAM"
echo
exit
fi
NORMALBAM=$1
TUMORBAM=$2
NBASE=$(basename $NORMALBAM | sed 's/.bam//')
TBASE=$(basename $TUMORBAM | sed 's/.bam//')
TAG=${TBASE}____${NBASE}
ODIR=scratch/$TAG
mkdir -p $ODIR
#bsub -We 59 -o LSF/ -e Err/ -J f_COUNT_$$_N -R "rusage[mem=40]" \
echo "Creating base counts for Normal Sample"
$SDIR/getBaseCountsZZAutoWithName.sh $ODIR/${NBASE}.dat $NORMALBAM
#bsub -We 59 -o LSF/ -e Err/ -J f_COUNT_$$_T -R "rusage[mem=40]"
echo "Creating base counts for Tumor Sample"
$SDIR/getBaseCountsZZAutoWithName.sh $ODIR/${TBASE}.dat $TUMORBAM
#bsub -We 59 -o LSF/ -e Err/ -n 2 -R "rusage[mem=60]" -J f_JOIN_$$ -w "post_done(f_COUNT_$$_*)" \
echo "Running mergeTN.py"
$SDIR/mergeTN.py $ODIR/${TBASE}.dat.gz $ODIR/${NBASE}.dat.gz | gzip -9 -c - >$ODIR/countsMerged____${TAG}.dat.gz
#bsub -We 59 -o LSF/ -e Err/ -J f_FACETS_$$ -w "post_done(f_JOIN_$$)" \
echo "Running FACETs"
Rscript $SDIR/r_scripts/doFacets.R $ODIR/countsMerged____${TAG}.dat.gz