refactor(benchmark): consolidate generated artifacts under run/ directory

Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
2026-08-29 00:19:31 +02:00
parent 54e4600120
commit 52f26809af
1057 changed files with 449 additions and 449 deletions
@@ -4,8 +4,9 @@
 set -euo pipefail

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

-for genome_file in "${SCRIPT_DIR}"/genomes/*.fna.gz; do
+for genome_file in "${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}"