snakejob

#!/usr/bin/env bash

display_help() {
  echo "Usage: ./snakejob -c config.yaml -u cluster.yaml"
  echo ""
  echo "Options:"
  echo "-c config file (--configfile)"
  echo "-u cluster config file"
  echo "-n dry run mode"
  echo ""
  exit 0
}

while getopts 'c:u:inh' flag; do
  case "${flag}" in
    c) config="${OPTARG}" ;;
    u) cluster="${OPTARG}" ;;
    n) dryrun="-n" ;;
    h) display_help
       exit 1 ;;
  esac
done

if [ ! -d "clusterlog" ]; then
  mkdir -p clusterlog
fi

if [ ! -z "$dryrun" ];then
	echo "dry run mode"
fi

if [ ! -e $config ]; then
	echo "error: config file does not exist" 
	exit 0
fi

if [ ! -e $cluster ]; then
  echo "error: cluster file does not exist" 
  exit 0
fi

echo config used is $config
echo cluster used is $cluster

bsub=("bsub -K -J $jname:{rule}:{wildcards}"
"-P acc_ad-omics "
"-q {cluster.queue} "
"-n {cluster.cores} -R \"span[hosts=1] select[mem>{cluster.mem}]"
"rusage[mem={cluster.mem}]\" -W {cluster.time} "
"-oo clusterlog/{rule}_{wildcards}.stdout "
"-eo clusterlog/{rule}_{wildcards}.stderr < ")

./snakeSV --configfile $config -pr --local-cores 1 --use-conda \
  -u $cluster --cluster-sync "${bsub[*]}" \
  --keep-going \
  --rerun-incomplete \
  --jobs 50 \
  --restart-times 0 \
  --latency-wait 30 \
  $dryrun