run_postprocessing

#!/bin/bash
ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
ABSOLUTE_PATH="$(dirname $ABSOLUTE_PATH)"

if [[ "$1" == "h" || "$1" == "-h" || "$1" == "-help" || "$1" == "--help" ]]; then
    echo "Usage: ./run_postprocessing OPTION1=value1 OPTION2=value2 ..."
    echo "OPTIONs:"
    echo "    VL      : viremic viral load threshold           [default: 1000]"
    echo "    STANWAY : either (r)stan or cmdstan              [default: cmdstan]"
    echo "    ALPHA   : sd for alpha prior in GP               [default: 1]"
    echo "    SHARE   : whether gp hyper needs sharing         [default: TRUE]"
    echo "    DEPENDS : list of queue id this job depends on   [default: ]"
    echo "    LOCAL   : run the analysis locally?              [default: TRUE]"
    echo "    INDIR   : directory where github directory is located"
    echo "    OUTDIR  : directory where output will be saved"
    exit 0
fi

for ARGUMENT in "$@"
do
   KEY=$(echo $ARGUMENT | cut -f1 -d=)

   KEY_LENGTH=${#KEY}
   VALUE="${ARGUMENT:$KEY_LENGTH+1}"

   echo "export $KEY=$VALUE"
   export "$KEY"="$VALUE"
done

# default options
VL="${VL:-1000}" 
FTP="${FTP:-FALSE}"
ALPHA="${ALPHA:-1}"
SHARE="${SHARE:-FALSE}"
STANWAY="${STANWAY:-cmdstan}"
INDIR="${INDIR:-$ABSOLUTE_PATH}"
OUTDIR="${OUTDIR:-/rds/general/user/ab1820/home/projects/2022/longvl}"
LOCAL="${LOCAL:-TRUE}"

#################
# OPTION CHECKS #
#################

# stop if STANWAY is not stan or cmdstan
if [[ ! "$STANWAY" =~ ^(stan|cmdstan)$ ]]; then
    echo "STANWAY must be either stan (rstan) or cmdstan (cmdstanr)."
    exit 1
fi
# stop if SHARE is not True, TRUE, T, False, FALSE, F
if [[ ! "$SHARE" =~ ^(TRUE|FALSE)$ ]]; then
    echo "SHARE must be either TRUE or FALSE."
    exit 1
fi
echo "Selected options:"
echo "  VL = $VL"
echo "  STANWAY = $STANWAY"
echo "  INDIR = $INDIR"
echo "  OUTDIR = $OUTDIR"
echo "  SHARE = $SHARE"
echo "  LOCAL = $LOCAL"

# "build" jobname and envname
ENVNAME="longivl"
ALPHA2=$(echo "$ALPHA" | sed 's/\.//')
if [[ "$SHARE" == "TRUE" ]]; then
    ALPHA2="${ALPHA2}sharedhyper"
fi
JOBNAME="alpha${ALPHA2}_vl_$VL"
if [[ "$STANWAY" == "cmdstan" ]]; then
	JOBNAME="${STANWAY}_${JOBNAME}"
	ENVNAME="${ENVNAME}_cmdstan"
fi
if [[ "$FTP" == "TRUE" ]]; then
    JOBNAME="$JOBNAME"_firstpart
fi
echo "  JOBNAME = $JOBNAME"

HEAD="#!/bin/sh
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=1:ompthreads=1:mem=99gb
#PBS -j oe
#PBS -N p-$JOBNAME
module load anaconda3/personal
source activate $ENVNAME

set -euo pipefail
"

SUBMIT_CMD="qsub"

if [[ "$LOCAL" == "TRUE" ]]; then
    HEAD="#!/bin/sh
    conda activate $ENVNAME"
    SUBMIT_CMD="sh"
fi



cat > $OUTDIR/bash-$JOBNAME-joint_postprocessing.pbs <<EOF
$HEAD
INDIR=$INDIR
OUTDIR=$OUTDIR
JOBNAME=$JOBNAME
#
# only add the joint prefix if $SHARE is FALSE: 
JOBNAME_JOINT="$JOBNAME"
if [[ "$SHARE" == "FALSE" ]]; then
    JOBNAME_JOINT="$JOBNAME"_joint
fi

  
Rscript \$INDIR/scripts/VL_jointpostprocessing.R \\
    --viremic-viral-load $VL \\
    --jobname \$JOBNAME \\
    --outdir \$OUTDIR/\${JOBNAME_JOINT} \\
    --indir \$OUTDIR \\
    --shared-hyper $SHARE

Rscript \$INDIR/scripts/VL_make_paper_figures.R \\
    --viremic-viral-load $VL \\
    --jobname \$JOBNAME \\
    --outdir \$OUTDIR/\${JOBNAME_JOINT} \\
    --indir \$OUTDIR \\
    --shared-hyper $SHARE

Rscript -e "
rmarkdown::render(
    '\$INDIR/scripts/VL_postprocessing_make_report.Rmd',
    params=list(indir='\$OUTDIR', jobid='\$JOBNAME'),
    output_dir='\$OUTDIR/\${JOBNAME_JOINT}')
"

EOF

cd $OUTDIR

if [[ ! -z "$DEPENDS" ]]; then
    DEPENDS="-W depend=afterok:$DEPENDS"
fi

$SUBMIT_CMD $DEPENDS bash-$JOBNAME-joint_postprocessing.pbs