pipeline

#!/usr/bin/env bash
#
# Copyright © 2022 Ye Chang yech1990@gmail.com
# Distributed under terms of the GNU license.
#
# Created: 2022-04-04 18:49

logo="
\033[1;34m ███╗   ███╗ ██████╗  █████╗       ███████╗ █████╗  ██████╗███████╗███████╗ ██████╗  \033[0m
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\033[1;34m ██╔████╔██║███████╗ ███████║█████╗███████╗███████║██║     ███████╗█████╗  ██║   ██║ \033[0m
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\033[1;34m ██║ ╚═╝ ██║╚██████╔╝██║  ██║      ███████║██║  ██║╚██████╗███████║███████╗╚██████╔╝ \033[0m
\033[1;34m ╚═╝     ╚═╝ ╚═════╝ ╚═╝  ╚═╝      ╚══════╝╚═╝  ╚═╝ ╚═════╝╚══════╝╚══════╝ ╚══▀▀═╝  \033[0m
\033[1;34m                                                                                     \033[0m
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"

printf "$logo\n"

# Set default values
snake="/opt/pipeline/Snakefile"
conf="data.yaml"

POSITIONAL_ARGS=()
while [[ $# -gt 0 ]]; do
  case $1 in
  -j | --jobs | --cores)
    cores_cmd="$2"
    shift
    shift
    ;;
  -c | --conf)
    conf="$2"
    shift
    shift
    ;;
  -s | --snake)
    snake="$2"
    shift
    shift
    ;;
  *)
    POSITIONAL_ARGS+=("$1")
    shift
    ;;
  esac
done
set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters

if [ ! -f "${conf}" ]; then
  echo "${conf} can not be found!"
  exit 1
fi
if [ -z "${cores_cmd}" ]; then
  cores_conf=$(python -c 'import yaml, sys;print(yaml.safe_load(open(sys.argv[1],"r")).get("cores",""))' ${conf})
  if [ -z "${cores_conf}" ]; then
    cores=48
  else
    cores=${cores_conf}
  fi
else
  cores=${cores_cmd}
fi

panoptes --ip 0.0.0.0 --port 5000 1>/dev/null 2>/dev/null &
export PANOPTES_PID=$!
# echo "PANOPTES_PID=$PANOPTES_PID"
trap 'kill -s SIGKILL $PANOPTES_PID' EXIT
while true; do
  if curl -s http://127.0.0.1:5000/api/service-info | grep -q running; then
    echo -e "\033[0;32mPLEASE MONITOR THE PIPELINE AT\033[0m http://127.0.0.1:5000"
    echo -e "\033[0;32mIf you are running this pipeline on a remote server, \033[0m"
    echo -e "\033[0;32mreplace the IP adress with server IP, or set ssh proxy on you local machine.\033[0m"
    LOGFILE="SACSEQ_LOG_$(date +"%F-%H%M%S").txt"
    echo -e "\033[0;32mREAD DEBUG LOG AT\033[0m ${LOGFILE}"
    printf "\033[0;33m Analyzing...\033[0m"
    snakemake --wms-monitor http://127.0.0.1:5000 --rerun-incomplete --jobs ${cores} --snakefile ${snake} --configfiles /opt/pipeline/config.yaml ${conf} $@ 1>${LOGFILE} 2>${LOGFILE}
    if [ $? -eq 0 ]; then
      printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
      printf "\033[0;32m\xE2\x9C\x94\033[0m Successfully finished all jobs.\n"
    else
      printf "\033[0;33m\b\b\b\b\b\b\b\b\b\b\b\b\b\033[0m"
      printf "\033[0;31m\xE2\x9D\x8C\033[0m Jobs exit with error!\n"
    fi
    # rm .panoptes.db
    kill -s SIGKILL $PANOPTES_PID
    break
  fi
  echo "$(date) waiting for service to start..."
  sleep 2
done