RVDB_VERSION=19.0
mkdir -p ${RVDB_VERSION} && cd ${RVDB_VERSION}

# a place where temporary files will be written
RVDB_SCRATCH_DIR=$myscratchdir/rvdb${RVDB_VERSION}
# taxadb can be generated or downloaded (please refer to taxadb website)
taxadb=/my/databases/taxadb_full.sqlite
# the directory containing this readme file and the rvdb-prot scripts
rvdbPipeline=$HOME/my/bioinformatics/rvdb-prot/


RVDB_ORIG_DIR=${PWD}
wget https://rvdb.dbi.udel.edu/download/U-RVDBv${RVDB_VERSION}.fasta.gz
mkdir -p ${RVDB_SCRATCH_DIR}

# here is an example running snakemake with a slurm cluster manager, adapt it to your needs

slurmpartition="common"
slurmqos="normal"

# this variable is needed for snakemake to launch subsequent jobs
export sbcmd="sbatch --cpus-per-task={threads} --mem={cluster.mem} --partition={cluster.partition} --qos={cluster.qos} --out={cluster.out} --error={cluster.error} --job-name={cluster.name} {cluster.extra}"


sbatch --qos ${slurmqos} --partition ${slurmpartition} -c 1 --job-name=rvdb${RVDB_VERSION} --wrap="snakemake --rerun-incomplete --snakefile $rvdbPipeline/pipeline/Snakefile -p -pr --local-cores 1 --jobs 1000 --cluster-config $rvdbPipeline/slurm.json --cluster \"$sbcmd\" --config origNucl=${RVDB_ORIG_DIR}/U-RVDBv${RVDB_VERSION}.fasta.gz scratchDir=${RVDB_SCRATCH_DIR} sampleName=rvdb${RVDB_VERSION} taxadb=$taxadb prefix=U-RVDBv${RVDB_VERSION}"