File size: 3,800 Bytes
c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 504d922 c289d87 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | #!/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}"
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