Tamarind CLI

Command-line interface for the Tamarind Bio platform. Discover tools, submit and monitor protein / nucleic-acid / small-molecule jobs, and download results — from your terminal, a script, CI, or an AI coding agent (Claude Code, Codex, …).

The CLI is a thin client over the same API the Tamarind MCP server uses, so the two stay in lockstep. See docs/architecture.md for how drift is prevented.

Install

uv tool install tamarind-cli      # or: pipx install tamarind-cli

Or with the bootstrap installer (installs uv if needed):

curl -fsSL https://app.tamarind.bio/cli/install.sh | sh

To track the repo directly instead of the PyPI release:

uv tool install "git+https://github.com/Tamarind-Bio/tamarind-cli"
# or: pipx install "git+https://github.com/Tamarind-Bio/tamarind-cli"

Releasing: tag a GitHub Release and the publish.yml workflow builds and uploads to PyPI via Trusted Publishing (configure the trusted publisher for tamarind-cli on PyPI first).

Authenticate

Get an API key from the Tamarind web app (Settings → API), then either:

export TAMARIND_API_KEY="sk_..."      # best for agents / CI
# or
tamarind auth login                    # stores it in ~/.tamarind/config.json
tamarind auth status

Quickstart

# 1. Find a tool
tamarind tools --function structure-prediction --modality protein
tamarind tools --search boltz

# 2. Inspect its parameters and grab a runnable example
tamarind schema boltz
tamarind schema boltz --example > job.yaml   # most tools ship an example; some don't

# 3. Validate, then submit
tamarind validate boltz --input job.yaml
tamarind submit   boltz --input job.yaml --name my-run --wait --download ./out

# 4. Monitor / fetch
tamarind jobs
tamarind status my-run
tamarind results my-run --download ./out

Set individual fields inline instead of a file:

tamarind submit boltz \
  --set inputFormat=sequence \
  --set sequence=MKTVRQERLKSIVRIL... \
  --name quick-fold

Output for agents

Every command emits JSON when stdout is not a TTY, or with --json. Exit codes are stable: 0 ok, 3 auth, 4 not-found, 5 validation, 6 rate-limit, 7 timeout (a --wait/--timeout deadline elapsed).

Not every tool ships a runnable example — schema <tool> --example exits non-zero (with a clear message) when one isn't available, so a > job.yaml redirect never silently produces an empty file. Destructive commands (delete, files delete) require --yes/-y when run non-interactively (piped or --json), so an agent never removes data without an explicit confirmation.

tamarind jobs --json | jq '.jobs[] | select(.JobStatus=="Running")'

Commands

Run tamarind <command> --help for full options.

Configuration

Profiles (key + endpoints) are stored in ~/.tamarind/config.json. Use a profile to point at staging:

tamarind --profile staging --api-base https://staging.tamarind.bio/api/ auth login
TAMARIND_PROFILE=staging tamarind tools

Links

• CLI docs — the hosted quickstart and command reference
• MCP server — the hosted option for claude.ai, ChatGPT, and other MCP clients
• API key — get your key and review rate limits

Questions or need help? Contact us at info@tamarind.bio.

License

Licensed under the Apache License 2.0.