---
name: cell2026-configuring
description: Use when the user wants to set up, configure, or troubleshoot cell2026 (Shinobu Lab) — SSH access, the embedding endpoint for docs search (RAG), or the ~/.hpc-agent/cell2026.json file. Also use when cell2026 tools fail with connection or embedding errors.
---

# Configuring cell2026 (Shinobu Lab)

Settings live in `~/.hpc-agent/cell2026.json` (the common directory
shared by every facility this plugin serves — one file per facility). Env
vars `CELL2026_HOST` and `CELL2026_EMBED_API_KEY` override the
file; the embedding key also falls back to a shared `RCCS_EMBED_API_KEY`
env var if several facilities share the same endpoint.

The file this facility needs (add `"embedding": {"api_key": "..."}` too if
docs search should use vector rather than keyword matching):

```json
{
  "ssh": {
    "host": "cell2026"
  }
}
```

## What must be true before it can connect

cell2026 requires non-interactive key-based SSH. Add a
'cell2026' alias to ~/.ssh/config using the hostname and username
issued by the lab, or set ssh.host to that user@host. There is no
public login hostname to guess. Use host=localhost when the agent
already runs on the head node. No project/account is configured:
neither scheduler uses one. CELL2026_DEFAULT_SCHEDULER may be
'gridengine' (the default) or 'slurm'; CELL2026_GE_BIN can name
the AGE binary directory if the login shell does not put it on PATH.

## Guided setup — interview the user, then write the file

Read the existing `~/.hpc-agent/cell2026.json` first and only ask
about what's missing or being changed.

1. **SSH** — ask how they reach this facility's login node:

cell2026 uses key-based SSH. Configure the hostname and username issued by the
lab as an SSH alias or user@host; no public hostname should be guessed. Use
`host=localhost` when the agent already runs on the head node. There are no
project/account settings.

`CELL2026_DEFAULT_SCHEDULER` may be `gridengine` (default) or `slurm`.
`CELL2026_GE_BIN` may point at the AGE binary directory when the login shell
does not put it on PATH. The optional embedding key uses the shared RIKEN
endpoint; without it, docs search falls back to BM25.

   - **Running the agent session directly on this facility's own
     front-end/login node** (not a personal laptop)? Use
     `"host": "localhost"` instead — no SSH key needed. Skip the
     verification step below for this case; there's nothing to probe.
   - Verify with: `ssh -o BatchMode=yes <host> 'echo ok'` (BatchMode
     matters — the server cannot answer a password prompt; key-based auth
     is required). Not applicable for `"host": "localhost"`.
   - **Enable SSH multiplexing unless the user explicitly opts out.** This
     lets repeated agent operations reuse one authenticated connection rather
     than making the login node authenticate every call. Recommend an SSH
     alias and, after showing the exact change and receiving confirmation,
     add a narrowly scoped block to `~/.ssh/config` without overwriting any
     unrelated entries:
     ```sshconfig
     Host <alias>
       ControlMaster auto
       ControlPath ~/.ssh/controlmasters/%C
       ControlPersist 30m
     ```
     Create `~/.ssh/controlmasters` with mode `0700`, then open the initial
     master in the user's own terminal with `ssh -MNf <alias>`. Set
     `ssh.host` to that same alias. `ControlMaster no` is an intentional
     opt-out; do not add or change multiplexing settings when it is present.
2. **Embedding API key** (optional — skippable; BM25 keyword search still
   works without it). Store it under `embedding.api_key`.
3. **Write the file** to `~/.hpc-agent/cell2026.json` (`mkdir -p
   ~/.hpc-agent` first if needed), then `chmod 600` it — it may hold an API
   key. Never commit it or echo the key back in conversation.
4. **Validate**:
   ```bash
   uv tool run --quiet --from git+https://github.com/william-dawson/hpc-rookery.git@main hpc-doctor cell2026
   ```
   (From a checkout of this repo: `.venv/bin/python -m hpc_mcp.doctor
   cell2026` also works.)
5. **If the embedding endpoint was added or changed**, rebuild this
   facility's docs index:
   ```bash
   uv tool run --quiet --from git+https://github.com/william-dawson/hpc-rookery.git@main python -m hpc_mcp.ingest cell2026
   ```
   Then run the doctor again — it should report "chunks with embeddings".

## Notes

- Settings are read fresh on every tool call, so a config file edit
  (including switching `ssh.host` to/from `"localhost"`) applies
  immediately — no server restart needed. A rebuilt docs index still needs
  the `hpc-docs` server restarted to be picked up.
- Off-network or without a key, docs search transparently falls back to
  BM25 keyword search over the same content — the plugin still works.