check_app4.sh

#!/bin/bash
set -a
#
################################################################
#
# CHECK APP4 SCRIPT FOR EASY JOB SUMMARIES
# 
# EXP/OUTPUTS CAN BE DEFINED; 
# OR CAN BE READ DIRECTLY FROM CUSTOM_APP4.SH (SET: READ_FROM_CUSTOM_WRAPPER=true)
#
################################################################
#
# USER OPTIONS

EXP_TO_PROCESS=HI-nl-C-05-r1
OUTPUT_LOC=/scratch/$PROJECT/$USER/APP4_output
# OR
READ_FROM_CUSTOM_WRAPPER=false

################################################################
#
USER=$USER
if [[ $MODE == "production" ]]; then
  EXP_TO_PROCESS=$1
else
  MODE=custom
  if $READ_FROM_CUSTOM_WRAPPER; then
    check_app4=true
    source ./custom_app4.sh
  fi
fi

#
# Set up environment
source ./subroutines/setup_env.sh
# Run completion check
echo "custom-mode APP4 checking tool"
echo "completion checking exp ${EXP_TO_PROCESS}..."
python ./subroutines/completion_check.py --multi
echo ""
grep "file name does not match expected" $JOB_OUTPUT
echo -e "\ncompleted quality checking exp ${EXP_TO_PROCESS}"