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pipeio_dag_export SVG fails with Permission denied on dot

After installing graphviz in the rag env, pipeio_dag_export(flow="preprocess_ieeg", graph_type="rulegraph", output_format="svg") still fails:

[Errno 13] Permission denied: 'dot'

The MCP server process may not see the newly installed binary (PATH not updated), or it may need to use conda run -n rag dot instead of bare dot. The mermaid export works fine.

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

6b295b2 Update badlabel audit note: full pipeline comparison (85 new vs 7 legacy vs 71 TTL), zarr fix confirmed, 97.2% TTL catch rate
a532476 Fix zarr write bug in feature.py: include coordinate variables in chunk encoding
9cb9de5 Update badlabel audit result note with pipeline run findings: LNR useless after lowpass, zarr v3 write bug

README:

type: readme

Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha
  • issue-arash-20260409-232034-115590.md — Both involve MCP server environment issues — pipeio_nb_exec runs in wrong env, and pipeio_dag_export can't find dot because MCP server PATH differs from the rag env where graphviz was installed
  • issue-arash-20260409-232128-727233.md — Related pipeio_run environment/invocation issues — flags not passed correctly to snakemake, similar class of MCP-to-subprocess environment problems
  • issue-arash-20260409-232102-577698.md — Another pipeio runtime failure (run_status crash), same session cluster of pipeio infrastructure issues