auto_resubmit_rev_sf.job

#!/bin/bash
#PBS -N approx_raider
#PBS -m abe
#PBS -M "schaefce@miamioh.edu"
#PBS -l nodes=1:ppn=8
#PBS -l walltime=4:0:0
##PBS -l qos=preemptor


cd ~/karro/RAIDER_eval/

sfile_base=aseed_files/aseeds
sfile_orig=${sfile}
sfile=${sfile_base}/${sfile}

seed=$(head -n 1 ${sfile})
weight=$(grep -o "1" <<< "$seed" | wc -l)
L=${#seed} 
basedata=${data##*/}
id=$(basename $sfile .txt)

fname=${dir}/F${freq}_${id}

if [ -z $CP ]; then
    CP=false
fi

if [ $CP = false ]; then
    CP_str=""
else
    CP_str="--cp"
fi

if [ ${type} == "chrom_sim" ]; then
    ./RAIDER_eval.py -R --R2 --AR --RS --nuke -r $fname -f ${freq} --sf ${sfile} --pwt ${WT} ${CP_str} --stats_only chrom_sim ${data} 
else
    ./RAIDER_eval.py -R --nuke -r $fname -f ${freq} --sf ${sfile} --pwt ${WT} ${CP_str} --stats_only seq_files ${data} 
fi

check_fname='reval.dat'
RSAVE_CHECKFILE=${fname}/${check_fname}
log_fname='reval.log'
RSAVE_LOG=${fname}/${log_fname}

echo "Output directory: ${fname}"
echo "Data: ${basedata}"
echo "Seed: ${seed}"

if [ -n "$RSAVE_STEP"  ]; then
    RSAVE_STEP=`expr $RSAVE_STEP + 1`
else
    RSAVE_STEP=0
fi

echo "RSAVESTEP: ${RSAVE_STEP}"

if [ -f "${RSAVE_CHECKFILE}" ]; then
    OLD_CHECKFILE=${RSAVE_CHECKFILE}.old
    OLD_LOG=${RSAVE_LOG}.old
    if [ -f $OLD_CHECKFILE ]; then
        mv $OLD_CHECKFILE $RSAVE_CHECKFILE.$RSAVE_STEP
    fi
    if [ -f $OLD_LOG ]; then
        mv $OLD_LOG $RSAVE_LOG.$RSAVE_STEP
    fi
fi


#
# Check if the job is finished and if it is not
# resubmit this file
#
if grep CONTINUE ${RSAVE_LOG} 
    then
        ssh c-0-0 "cd ~/karro/RAIDER_eval/; qsub -v dir=$dir,sfile=$sfile_orig,freq=$freq,type=$type,data=$data,RSAVE_STEP=$RSAVE_STEP,WT=$WT,CP=true auto_resubmit_rev_sf.job"
elif grep FINISHED ${RSAVE_LOG}
    then
        #dir=${fname} ./cleanup.sh
        ./doSortedAnalysis.R -f ${fname}/stats.txt --formula=~+tpr -v --auto_out
else
    echo "error - no continue or finished"
fi

#exit 0