Eric Coissac
26026288de
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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
14 lines
516 B
Bash
Executable File
14 lines
516 B
Bash
Executable File
#!/usr/bin/env bash
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# Simulate all genomes. Delegates to simulate_one.sh per genome.
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# Prefer running via `gmake simulate` which handles individual dependencies.
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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RUN_DIR="${SCRIPT_DIR}/run"
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for genome_file in "${RUN_DIR}"/genomes/*.fna.gz; do
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out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
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--dir-for "${genome_file}")
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bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
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done
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