Optional AI agent¶
SAMWISE includes a beta OpenAI-based AI agent for interrogating genomes and their metabolisms from files in an output directory. It is separate from the Nextflow workflows, is not activated by default, and is optional.
For the agent's original setup notes, see the
agent/README.md.
From the agent/ directory, create the environment:
Copy the example environment file and set the API key and user settings locally:
Run the agent from agent/ with:
The agent is an analysis assistant, not a Nextflow orchestrator: it does not
start or manage SAMWISE workflow runs. It can inspect files under the roots in
ALLOWED_ROOTS and can write an explicitly requested, approved module only to
the locations configured in MODULE_WRITE_ROOTS; those capabilities are
disabled or restricted by local configuration. It is usable only after the
environment, provider settings, and Python launcher have been explicitly
configured and activated. SAMWISE's core workflows do not require the agent.
.env is local configuration and must not be committed. Never commit API
keys, access tokens, credentials, private datasets, or generated conversation
memory. Follow the contribution guide
and security policy
for repository security practices.