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):

brew install smartsbio/tap/smarts

macOS / Linux (install script):

curl -fsSL https://smarts.bio/install.sh | sh

Windows (PowerShell):

irm https://smarts.bio/install.ps1 | iex

With Cargo (any platform with Rust):

cargo install smarts-cli

Authenticate

smarts login

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

Reproducible pipelines

Save a finished run as a reusable pipeline spec and re-run it on different files. Spec paths prefixed with @ are in the workspace; otherwise an existing local file (e.g. one in your repo) is used.

# Built-in pipelines plus the ones saved in this workspace
smarts pipeline list

# Inputs and steps of a built-in id, a saved spec, or a local .json file
smarts pipeline show <id|path>

# Save a finished run to pipelines/specs/<name>.pipeline.json
smarts pipeline save <runId> --name my-pipeline      # --force replaces an existing one

# Check a spec without running it (exits non-zero if invalid)
smarts pipeline validate @pipelines/specs/my-pipeline.pipeline.json

# Run a saved or local spec with new inputs
smarts pipeline run --spec @pipelines/specs/my-pipeline.pipeline.json --param inputBam=input/sample2.bam

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.

MCP overview →Local MCP server →All integrations →