fix: resolve breaking issues in docking pipeline

[AJPreto]

Fixes three breaking issues discovered during GPU docking runs (Boltz2 + DiffDock):

1. Makefile - Expand LD_LIBRARY_PATH with nvidia CUDA library paths (cu13, cuda_nvrtc, cudnn, cublas) to fix DiffDock crashing with NVRTC_ERROR_COMPILATION at runtime.
2. scripts/run_guild.py - Add --no-decoys CLI flag so runs can proceed without a decoy file present.
3. guild/bulk.py - Boltz2 template robustness: import PROTEINS_FOLDER, prefer single-chain clean PDB as template, and retry without template on empty manifest.

All three fixes validated end-to-end on a GPU node.

[Copilot]

Pull request overview

This PR addresses runtime breakages observed during GPU docking runs by improving container CUDA library visibility, adding a CLI option to skip decoys, and making Boltz2 templating more robust during bulk docking.

Changes:

• Add a --no-decoys flag to allow running the pipeline when a decoy file is unavailable.
• Improve Boltz2 template handling by preferring a single-chain cleaned PDB template and retrying without a template when Boltz produces an empty manifest.
• Extend LD_LIBRARY_PATH in Docker run targets to include additional NVIDIA CUDA-related shared library paths.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
scripts/run_guild.py	Adds --no-decoys CLI flag and wires it into BulkRun(use_decoys=...).
guild/bulk.py	Uses a single-chain cleaned PDB as the Boltz template and retries Boltz without a template when the manifest is empty.
Makefile	Updates GPU docker run targets to include additional NVIDIA library paths in LD_LIBRARY_PATH.

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[Copilot]

manifest.json is loaded without any error handling; if the file is truncated/invalid (e.g., Boltz interrupted mid-write) this will raise JSONDecodeError and abort the entire batch. Consider wrapping the manifest load in try/except and treating parse errors like an empty manifest (log + retry without template, or skip with warning).

Suggested change

	with open(manifest_path) as _mf:
	_manifest = _json.load(_mf)
	try:
	with open(manifest_path) as _mf:
	_manifest = _json.load(_mf)
	except (_json.JSONDecodeError, OSError) as exc:
	logger.warning(
	f"Boltz2 produced unreadable manifest for {run_id}: {exc}. "
	"Retrying without template..."
	)
	_manifest = {}

[Copilot]

The new Boltz empty-manifest retry path is complex and impacts run stability, but there are no unit tests exercising it. Since this repo already has BulkRun tests, consider adding a test that mocks deploy_boltz/generate_boltz_yaml and verifies a retry occurs when manifest.json has no records.

[Copilot]

LD_LIBRARY_PATH is fully hardcoded here and duplicated across multiple targets, which can drift from the value baked into the image and is easy to forget to update in one place. Consider factoring this into a Makefile variable and/or appending to the container’s existing LD_LIBRARY_PATH instead of replacing it entirely.

[Copilot]

LD_LIBRARY_PATH is duplicated here (and differs from the image’s ENV LD_LIBRARY_PATH), which increases the chance of future drift between targets/images. Consider reusing a single Makefile variable (shared with run-boltz) and/or appending to the existing container LD_LIBRARY_PATH rather than replacing it.