GeniOmics

Agent access

Let your Agent search workflows, runs and results

Connect Codex, WorkBuddy or another Agent to organization-scoped read-only access. Analysis setup and submission stay in the existing GeniOmics pages.

Three-minute setup

Connect GeniOmics to your Agent

Prepare one organization access token and organization ID. Give the Agent a remote MCP URL or REST base URL, then let it use the same analysis flow as a person.

Open platform

GeniOmics Agent Gateway

One permission model

REST, MCP and the in-platform Copilot share the same organization permissions and audit boundary. The Agent only reads information exposed by the platform.

01

Prepare credentials

Access token + organization ID

02

Add the entry point

Remote MCP or REST base URL

03

Find workflows and data

Confirm what this account can use

Connection options

Choose the entry point that matches your Agent

Keep your existing analysis workflow. Start with read-only queries; configuration and submission stay in the platform.

Recommended

Remote MCP

In Codex, WorkBuddy or another Agent that supports remote MCP, add the URL and two headers so it can discover the tools enabled in this deployment.

Universal HTTP

REST API

For Agents without MCP support, call catalog, run, result and evidence endpoints directly. Every request carries the access token and organization ID.

Same contract

In-platform Copilot

The in-platform Copilot reuses the same capability contract and audit boundary instead of maintaining a hidden toolset that differs from external Agents.

Quick setup

Configure three things, then verify the connection

Give this configuration to the Agent administrator or developer. The first acceptance command should be tools/list or a catalog query, never a run submission.

  1. 01

    Prepare an access token

    Create or obtain an organization access token and confirm it is scoped to the target organization. Never commit it to a repository.

  2. 02

    Configure the remote entry point

    MCP uses /api/v1/agent-gateway/mcp; REST uses /api/v1/agent-gateway. Always send both headers together.

  3. 03

    Let the Agent discover first

    Call tools/list, or use catalog?query=RNA to verify organization scope, response shape and available capabilities.

MCP client configurationPOST /mcp
{
  "mcpServers": {
    "geniomics": {
      "url": "${API_URL}/api/v1/agent-gateway/mcp",
      "headers": {
        "Authorization": "Bearer ${TOKEN}",
        "X-Organization-Id": "${ORG_ID}"
      }
    }
  }
}
REST verification requestGET /catalog
curl -H "Authorization: Bearer $TOKEN" \
  -H "X-Organization-Id: $ORG_ID" \
  "$API_URL/api/v1/agent-gateway/catalog?query=RNA"

For local or self-hosted deployments, set AGENT_GATEWAY_READ_ONLY=true and restart the API first. Submission, cancellation and downloads continue in the existing platform pages.

What an Agent can do

Give the Agent verifiable facts before recommendations

These capabilities are bound to organization permissions, field allowlists and evidence references, making them a safe first tool layer.

01

Discover workflow catalog

geniomics.catalog.search

Read workflow versions, data contracts, input requirements and availability within organization scope.

02

Read run state

geniomics.run.inspect

Read stages, progress, failure reasons and frozen manifest summaries without Worker or object-storage locators.

03

Read result evidence

geniomics.evidence.inspect

Inspect verified files, summary hashes and stable citations; downloads remain platform-authorized.

Release boundary

Connect quickly. Keep execution controlled.

This page describes an auditable read-only Agent connection. The Agent can find workflows and read task and result evidence; configuration, submission and downloads stay in the platform.

Open platform

Read-only preview, off by default

The Gateway must be explicitly enabled by a deployment administrator. Once enabled, an Agent can discover workflows and read run and result evidence; setup, submission and downloads stay in the platform.

The read-only flag must be enabled before an Agent can call catalog, run or evidence endpoints.
The current integration cannot fill or submit analysis, or download files directly.
Every read remains scoped to organization permissions and frozen manifest evidence.

Data, analyses and reports in one workspace

Start with your next analysis

Choose a built-in analysis, add data, and review the run settings. Bring an existing Nextflow project through the import path.

Start an analysis
Let your Agent search workflows, runs and results · GeniOmics