run_HPC_AOC.sh

#!/bin/bash

clear

echo "Analysis of Orthologous Collections (AOC)."
echo "@Author: Alexander G. Lucaci"
echo ""

# Set up the pipeline failure expectations.
set -euo pipefail

# Downloading hyphy-analyses.
FOLDER="hyphy-analyses"
URL="https://github.com/veg/hyphy-analyses.git"

if [ ! -d "$FOLDER" ] ; then
    git clone "$URL" "$FOLDER"
fi

#echo "--- Initialized --- "

echo "Creating 'logs' directory"
mkdir -p logs

echo "Executing HPC Snakemake command"

snakemake \
      -s Snakefile \
      --cluster-config cluster.json \
      --cluster "qsub -V -l nodes={cluster.nodes}:ppn={cluster.ppn} -q {cluster.name} -l walltime={cluster.walltime} -e logs -o logs" \
      --jobs 4 all \
      --rerun-incomplete \
      --keep-going \
      --reason \
      --latency-wait 60 \
      --use-conda

# End of file 


exit 0