galaxyproject / galaxyproject/loom

Agent can't run RNA STARSolo via galaxy_run_tool -- "Parameter 'genomeDir': requires a value, but no legal values defined"

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Description

Reported via Orbit beta feedback (0.3.1, macOS, DeepSeek provider).

An agent trying to run **RNA STARSolo** through `galaxy_run_tool` fails with a 400:

Run tool failed: Unexpected HTTP status code: 400:
{"err_msg": "Parameter 'genomeDir': requires a value, but no legal values defined", "err_code": 400008}

The agent retried several times -- some attempts errored on `genomeDir`, others eventually "Started tool", so it's inconsistent. `genomeDir` is STARSolo's reference-index selection; "no legal values defined" points at the tool being submitted without a resolvable reference-genome value (the run payload didn't carry a valid built-in index).

The reporter notes both failing attempts were on the DeepSeek model and plans to retry with another, so it may be model-dependent (a smaller model not discovering/supplying the required reference param). But the underlying gap is that agent-driven `galaxy_run_tool` can submit reference-requiring tools (STARSolo, STAR, etc.) without a valid `genomeDir`.

Worth deciding: should `galaxy_run_tool` surface required-but-unset select params (with their legal values) up front so the model picks one, rather than letting an invalid request through? Likely lives in the galaxy-mcp tool-input handling -- how required select params with dynamic options are presented to the model -- so this may end up routed to galaxy-mcp.

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