| #!/usr/bin/env bash |
| set -euo pipefail |
|
|
| ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)" |
| BUNDLE_DIR="${ROOT_DIR}/portable_rdock_pipeline" |
| STALE_BUNDLE_DIR="${ROOT_DIR}/portable_rdock_pipeline.stale.$$" |
|
|
| rm -rf "${STALE_BUNDLE_DIR}" 2>/dev/null || true |
| if [ -e "${BUNDLE_DIR}" ]; then |
| mv "${BUNDLE_DIR}" "${STALE_BUNDLE_DIR}" 2>/dev/null || true |
| fi |
| rm -rf "${BUNDLE_DIR}" 2>/dev/null || true |
| mkdir -p "${BUNDLE_DIR}/scripts" "${BUNDLE_DIR}/configs" "${BUNDLE_DIR}/data/examples" "${BUNDLE_DIR}/tests_minimal" "${BUNDLE_DIR}/docs" |
|
|
| cp -R "${ROOT_DIR}/docking_pipeline" "${BUNDLE_DIR}/docking_pipeline" |
| cp -R "${ROOT_DIR}/libs" "${BUNDLE_DIR}/libs" |
| find "${BUNDLE_DIR}/libs/docking" -type f -name "backend_*mina.py" -delete |
| rm -f "${BUNDLE_DIR}/libs/benchmark/redocking_validation.py" |
| rm -f "${BUNDLE_DIR}/libs/docking/backend_haddock.py" |
| cp "${ROOT_DIR}/scripts/prepare_pdb_ligand_dataset.py" "${BUNDLE_DIR}/scripts/prepare_pdb_ligand_dataset.py" |
| cp "${ROOT_DIR}/scripts/download_example_smiles.py" "${BUNDLE_DIR}/scripts/download_example_smiles.py" |
| cp "${ROOT_DIR}/scripts/find_pdb_ligand_candidates.py" "${BUNDLE_DIR}/scripts/find_pdb_ligand_candidates.py" |
| cp "${ROOT_DIR}/scripts/run_strategy_benchmark_server.sh" "${BUNDLE_DIR}/scripts/run_strategy_benchmark_server.sh" |
| cp "${ROOT_DIR}/scripts/slurm_prepare_500k_dataset.sh" "${BUNDLE_DIR}/scripts/slurm_prepare_500k_dataset.sh" |
| cp "${ROOT_DIR}/scripts/slurm_smoke_500k_ablation.sh" "${BUNDLE_DIR}/scripts/slurm_smoke_500k_ablation.sh" |
| cp "${ROOT_DIR}/scripts/slurm_regressor_ablation_500k.sh" "${BUNDLE_DIR}/scripts/slurm_regressor_ablation_500k.sh" |
| cp "${ROOT_DIR}/scripts/slurm_strategy_benchmark_500k.sh" "${BUNDLE_DIR}/scripts/slurm_strategy_benchmark_500k.sh" |
| cp "${ROOT_DIR}/scripts/build_portable_bundle.sh" "${BUNDLE_DIR}/scripts/build_portable_bundle.sh" |
| cp "${ROOT_DIR}/configs/multifidelity_defaults.yaml" "${BUNDLE_DIR}/configs/multifidelity_defaults.yaml" |
| cp "${ROOT_DIR}/configs/reference_free_triage_bandit_defaults.yaml" "${BUNDLE_DIR}/configs/reference_free_triage_bandit_defaults.yaml" |
| cp "${ROOT_DIR}/configs/known_good_pdb_complexes.yaml" "${BUNDLE_DIR}/configs/known_good_pdb_complexes.yaml" |
| cp "${ROOT_DIR}/data/examples/example_smiles.smi" "${BUNDLE_DIR}/data/examples/example_smiles.smi" |
| cp "${ROOT_DIR}/data/examples/example_smiles_1000.smi" "${BUNDLE_DIR}/data/examples/example_smiles_1000.smi" |
| cp "${ROOT_DIR}/data/examples/example_pdb_dataset_config.yaml" "${BUNDLE_DIR}/data/examples/example_pdb_dataset_config.yaml" |
| if [ -d "${ROOT_DIR}/data/examples/rdock_3ptb_pubchem_50k_collect_only" ]; then |
| cp -R "${ROOT_DIR}/data/examples/rdock_3ptb_pubchem_50k_collect_only" "${BUNDLE_DIR}/data/examples/" |
| fi |
| cp "${ROOT_DIR}/environment.yml" "${BUNDLE_DIR}/environment.yml" |
| cp "${ROOT_DIR}/setup_server.sh" "${BUNDLE_DIR}/setup_server.sh" |
| cp "${ROOT_DIR}/check_environment.sh" "${BUNDLE_DIR}/check_environment.sh" |
| cp "${ROOT_DIR}/README_SERVER.md" "${BUNDLE_DIR}/README_SERVER.md" |
| cp -R "${ROOT_DIR}/docs/." "${BUNDLE_DIR}/docs/" |
| rm -f "${BUNDLE_DIR}"/docs/pipeline_methodology_fix_report_*.txt |
| rm -f "${BUNDLE_DIR}"/docs/plip_analog_run_report_*.txt |
| rm -rf "${BUNDLE_DIR}/tests_minimal" |
| cp -R "${ROOT_DIR}/tests_minimal" "${BUNDLE_DIR}/tests_minimal" |
|
|
| find "${BUNDLE_DIR}" -name "__pycache__" -type d -prune -exec rm -rf {} + |
| find "${BUNDLE_DIR}" -name "*.pyc" -delete |
| find "${BUNDLE_DIR}" -name ".DS_Store" -delete |
| rm -rf "${BUNDLE_DIR}/rdock" |
| rm -rf "${STALE_BUNDLE_DIR}" 2>/dev/null || true |
|
|
| removed_backend_token="s""mina" |
| if grep -RIl "${removed_backend_token}" "${BUNDLE_DIR}" >/tmp/portable_removed_backend_refs.txt; then |
| echo "ERROR: removed backend references remain in portable bundle:" >&2 |
| cat /tmp/portable_removed_backend_refs.txt >&2 |
| exit 1 |
| fi |
|
|
| echo "Built portable bundle at ${BUNDLE_DIR}" |
|
|
