obikmer/benchmark/simulate.sh

#!/usr/bin/env bash
# Simulate all genomes. Delegates to simulate_one.sh per genome.
# Prefer running via `gmake simulate` which handles individual dependencies.
set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
RUN_DIR="${SCRIPT_DIR}/run"

for genome_file in "${RUN_DIR}"/genomes/*.fna.gz; do
    out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
        --dir-for "${genome_file}")
    bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
done