snakejob

#!/usr/bin/env bash
# -m {cluster.partition}"
source activate snakemake
set -e

if [ ! -d "cluster" ]; then
  mkdir cluster
fi

curdir="$(pwd)"
jname="$(basename $curdir)"

config=$1

if [ ! -e $config ]; then
	config_file=config.yaml
else
	config_file=$config

fi

# use bash getopt to use short flags
config='config.yaml'
snakefile='Snakefile'
dryrun=""

print_usage() {
  printf "Usage: ./snakejob -c config.yaml -s Snakefile\nOptions:\n\t-c config file\n\t-s Snakefile\n\t-n dry run mode\n\t-m mode [eQTL/sQTL]\n\t-i interaction mode (requires interaction file in config.yaml)\n"
}

while getopts 'c:s:m:inh' flag; do
  case "${flag}" in
    c) config="${OPTARG}" ;;
    s) snakefile="${OPTARG}" ;;
    n) dryrun="-n" ;;
    h) print_usage
       exit 1 ;;
  esac
done


echo config used is $config
echo snakefile used is $snakefile

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 $snakefile ]; then
	echo "error: snakefile does not exist"
	exit 0
fi

#exit 0 

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

snakemake -u cluster.yaml --cluster-sync "${bsub[*]}" \
  --local-cores 4 --max-jobs-per-second 5 \
  --keep-going \
  --jobs 1000 \
  --restart-times 3 \
  -s $snakefile --configfile $config \
  --latency-wait 30 --rerun-incomplete \
  $dryrun \