Command-line interface

smarts is a single, self-contained binary that brings the smarts.bio agent, tools, pipelines, and workspace files to your terminal, scripts, and coding agents — on macOS, Linux, and Windows. No runtime to install.

Install

macOS / Linux (Homebrew):

macOS / Linux (install script):

Windows (PowerShell):

With Cargo (any platform with Rust):

Authenticate

Log in with your browser — a device-code flow that also works over SSH:

For CI or headless use, set an API key instead (generate one at chat.smarts.bio → Organization Settings → API Keys):

smarts auth set-key sk_live_...
# or:  export SMARTSBIO_API_KEY=sk_live_...

Core commands

The grammar is smarts <noun> <verb>. A few of the most common:

# Ask the agent (streams progress, then the answer)
smarts query "What is the function of the HBB gene?"

# Tools — discover and run
smarts tool list
smarts tool run ncbi-blast --param sequence=ATGGTGCACCTG...

# Pipelines — start a run and watch it to completion
smarts pipeline list
smarts pipeline run quality-control --param input=reads.fastq
smarts run watch <runId>

# Workspace files (shell-like; stays inside your workspace)
smarts file ls
smarts file cd results
smarts file upload ./local.vcf
smarts file open results.vcf        # opens in the browser viewer

# Open a LOCAL file in the viewer without uploading it
smarts open ./petri.jpeg

Pick a workspace

Most commands act on your default workspace. List them and set a default:

smarts workspace list
smarts workspace use <workspaceId>

Use it from an AI agent

The CLI ships a local MCP server, so Claude Desktop, Claude Code, Cursor, and other MCP clients can drive smarts.bio directly. See the local MCP guide.