galaxyproject / galaxyproject/loom

Agent over-thinks simple Galaxy tool-availability questions until the user has to abort

Open
#319 0 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
TypeScript
Stars
14
Forks
12
Avg merge
6d 5h
Merged PRs (30d)
17

Description

### Observed
Asking a direct, answerable question like "What tools are available and installed on Galaxy to annotate viral genomes?" causes multiple models to think for a very long time -- long enough that the user gives up and aborts the session. That question maps cleanly onto a single Galaxy MCP lookup (`search_tools_by_keywords` / `search_tools_by_name`), not something that should require extended reasoning.

### Expected
For straightforward tool-availability / catalog questions, the agent should route quickly to the Galaxy tool-search MCP and answer, rather than burning a long thinking budget before (or instead of) calling the obvious tool.

### Hypothesis / levers (both loom-side)
1. The always-on system prompt + full tool surface may be too heavy for the model to dispatch quickly -- the territory of #99 (right-size the system prompt + tool surface for smaller/open models).
2. There may be no steering nudging "for tool-availability questions, just call `search_tools_*`." `extensions/loom/context.ts` already references tool search, so a concise routing hint could short-circuit the over-reasoning.

Recommend linking #99 as the systemic fix and considering a targeted steering nudge for catalog/availability questions as the cheap mitigation.

### Environment
Orbit 0.3.1, macOS arm64, provider google / gemini-3.5-flash. Reported as affecting "multiple models," so likely not provider-specific.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reading extensions/loom/context.ts and the routing around the Galaxy MCP functions search_tools_by_keywords and search_tools_by_name. Compare the issue with #99 and determine whether a targeted steering hint is appropriate; done means straightforward tool-availability questions reach the tool search promptly without extended reasoning, with relevant behavior covered by the project's existing validation.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
ai, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.