CLI

Submit folding jobs from the terminal with the FastFold CLI.

The FastFold CLI is ideal for quick experiments, shell scripts, and CI pipelines.

Authentication

The CLI uses the same API key as the SDK.

export FASTFOLD_API_KEY="sk-...your-api-key"

You can also pass an API key explicitly via --api-key.

Submit a folding job

fastfold fold --sequence "LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES" --model boltz-2

On success, the CLI prints the created job ID to stdout.

Common flags

fastfold fold \
  --sequence "..." \
  --model boltz-2 \
  --name "My Job" \
  --api-key "sk-..." \
  --base-url "https://api.fastfold.ai"

CI-friendly pattern

If you want to keep the API key out of shell history, prefer environment variables:

export FASTFOLD_API_KEY="$FASTFOLD_API_KEY"
fastfold fold --sequence "$SEQ" --model boltz-2 --name "ci-$GITHUB_RUN_ID"

Next steps

For “wait for completion”, artifacts, and metrics workflows, use the Python SDK examples: /docs/developer/python-examples

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Recipes & Examples

Reference workflows by job type (single-sequence, complex/ligand, non-complex indexing, artifacts, metrics, fetch-by-id).

Troubleshooting

Common issues and fixes when using the FastFold Python SDK and CLI.

On this page

Authentication Submit a folding job Common flags CI-friendly pattern Next steps