run_snakemake.sh

#!/bin/bash

#SBATCH --ntasks=2
#SBATCH --mem=10gb
#SBATCH --time=24:00:00

source ~/.bashrc
source activate pm_env

cd $SLURM_SUBMIT_DIR
#cd /xdisk/bhurwitz/mig2020/rsgrps/bhurwitz/planet-microbe-functional-annotation

if [ -f results/interproscan.txt ]; then
    echo "removing interproscan.txt"
    rm results/interproscan.txt 
fi
if [ -f results/killed_interproscan.txt ]; then
    echo "removing killed_interproscan.txt"
    rm results/killed_interproscan.txt  
fi
#dry run
#snakemake -n

snakemake --unlock

echo 'snakemake --cluster "sbatch -A {cluster.group} -p {cluster.partition} -n {cluster.n} -t {cluster.time} -N {cluster.N} -mem={cluster.m} -e {cluster.e} -o {cluster.o}"  --cluster-config config/cluster.yml -j 30 --latency-wait 30'

#run in cluster
snakemake --cluster "sbatch -A {cluster.group} -p {cluster.partition} -n {cluster.n} -t {cluster.time} -N {cluster.N} --mem={cluster.m} -e {cluster.e} -o {cluster.o}"  --cluster-config config/cluster.yml -j 30 --latency-wait 30