Agent Setup

The recommended install path is agent-driven. The canonical source is INSTALL_FOR_AGENTS.md in the Genomi repository; this page summarizes the current flow.

Paste this into your agent

Open a local-capable AI agent and paste:

Install and configure Genomi by following the instructions here:
https://raw.githubusercontent.com/exon-research/genomi/master/INSTALL_FOR_AGENTS.md

The agent should fetch that file first, ask one question at a time, assemble a single installer command, run it, and verify the host MCP configuration.

What the agent asks

The install guide has three required user choices:

The recommended library choice is everything unless disk, time, or bandwidth is constrained. A full default install is about 7 GB. msigdb-hallmark is optional and requires a user-supplied MSigDB GMT export because its license does not allow redistribution.

Installer command shape

The agent resolves your answers into:

export GENOMI_HOME=<chosen-data-root>
python3 scripts/install_for_agents.py \
  --libraries <chosen-purpose-or-library-list> \
  [--genomi-home <chosen-data-root>] \
  [--genome-source /path/to/source] \
  [--user-nickname "Name"] \
  [--set-default-user]

The installer:

• installs the Genomi Python package,
• creates the stable command shim at <GENOMI_HOME>/bin/genomi,
• downloads the selected public reference libraries,
• imports a genome source when --genome-source is supplied,
• links the Genomi host skill and per-capability skills into detected host skill directories,
• writes or merges MCP config for supported hosts,
• verifies the install with the new command shim.

MCP server

The MCP server command is:

genomi serve

When using the installer-created shim, a host config usually points at:

{
  "mcpServers": {
    "genomi": {
      "command": "/absolute/path/to/GENOMI_HOME/bin/genomi",
      "args": ["serve"]
    }
  }
}

The installer knows the config schemas for Claude Code, Gemini CLI, Codex CLI, Hermes, and OpenClaw. If it cannot find a known host config directory, add the MCP entry manually with the same command and arguments.

Optional genome import

Genome import is optional. If you provide a local source path in the install conversation, that is approval for Genomi to read that source in that session and parse it into an Active Genome Index.

Supported source types

Do not paste genome contents into chat. Give the local file path.

Downloading raw data

If you do not have a raw DNA file yet, download it from the account you used to order testing and put the file in a local Genomi working folder.

If your file is zipped, leave it zipped. Genomi handles the common compressed formats.

Verify

After the installer completes:

• Reload the host MCP server.
• Ask the host to list installed skills or tools.
• Confirm the Genomi MCP entry runs genomi serve.
• If source code changed during a later update, restart the host agent and reload the Genomi MCP server.

Update

Use the stable Genomi command, not an MCP tool:

genomi install

genomi install and genomi update are the same command, and it updates everything that can be updated: it git-pulls the runtime, then checks each installed reference library against its upstream source and re-downloads only what actually changed (rolling sources like ClinVar pick up new releases; unchanged caches transfer nothing), and fetches any missing libraries in the selected set. It defaults to the everything selection. Pass --force to re-download unconditionally regardless of freshness.

If the JSON result reports that the source checkout changed, restart the host agent and reload the Genomi MCP server before continuing.