fastfold-agent-cli 0.0.44

Fastfold CLI — An autonomous agent for drug discovery research

Fastfold Agent CLI

Where scientists and AI agents work together doing real science.

Ask questions in natural language. Fastfold CLI plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions. Integrates with Fastfold AI Cloud for GPU compute, protein folding, workflow orchestration, and team collaboration.

Built on top of Claude Agent SDK and CellType CLI.

Prerequisites

• Python 3.10+ (recommended: let uv install managed interpreters).
• uv — install from the Astral docs: Installing uv. Quick options:

  • macOS / Linux (standalone installer):

    curl -LsSf https://astral.sh/uv/install.sh | sh
    

  • Windows (PowerShell):

    powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
    

    Alternatively: winget install --id=astral-sh.uv -e (see Astral docs for other methods).

    After installing uv, close and reopen your terminal or PowerShell so PATH picks up the uv executable.

Quick install

Requires Python 3.10+ and prerequisites above.

uv tool install "fastfold-agent-cli[all]" --python 3.10

Windows users — prefer WSL2 + Ubuntu ([all]): tiledbsoma does not publish usable native Windows wheels, so [all] on cmd/PowerShell usually fails. Install Windows Subsystem for Linux following Microsoft’s guide: Install WSL (recommended default distro Ubuntu), open an Ubuntu terminal, install uv + Python there, then run uv tool install "fastfold-agent-cli[all]" --python 3.10 inside WSL.

Staying on native Windows cmd/PowerShell: use [win_build] instead of [all] (same stack minus scanpy / cellxgene-census / tiledbsoma), or explicitly. Claude Code ships inside claude_agent_sdk, so uv tool install is normally enough — no npm on Linux/mac. On native Windows, CLI ≥ 0.0.41 validates real launcher spawnability and auto-fixes short launcher cache paths (fastfold setup, fastfold autofix, or interactive /autofix) to avoid WinError 206 from deep site-packages; ≥ 0.0.37 also prefers claude on PATH if you install @anthropic-ai/claude-code. Fallbacks: set UV_TOOL_DIR shorter before reinstall, or FASTFOLD_CLAUDE_CODE_CLI.

uv tool install "fastfold-agent-cli[chemistry,biology,ml,analysis]" --python 3.10

Convenience extra (CLI ≥ 0.0.38 on PyPI; Windows uv‑only installs use a short‑path bundled copy automatically):

uv tool install "fastfold-agent-cli[win_build]" --python 3.10

Authentication

# Interactive setup wizard (recommended)
# Choose provider(s) first (interactive toggle list), then enter keys
fastfold setup

# Or choose provider(s) explicitly (comma-separated)
fastfold setup --provider anthropic
fastfold setup --provider openai
fastfold setup --provider anthropic,openai

# Or set directly
export ANTHROPIC_API_KEY="sk-ant-..."
export OPENAI_API_KEY="sk-..."
export FASTFOLD_API_KEY="sk-..."

# Non-interactive (CI/scripting)
fastfold setup --api-key sk-ant-... --fastfold-api-key sk-...
fastfold setup --provider openai --openai-api-key sk-... --fastfold-api-key sk-...

Provider selection:

fastfold config set llm.provider anthropic
fastfold config set llm.model claude-sonnet-4-5-20250929
fastfold config set llm.anthropic_api_key sk-ant-...

fastfold config set llm.provider openai
fastfold config set llm.model gpt-4o
fastfold config set llm.openai_api_key sk-...

# Legacy fallback (Anthropic only, still supported)
fastfold config set llm.api_key sk-ant-...

Getting Started

# Start interactive session
fastfold

# Single query
fastfold "What are the top degradation targets for this compound?"

# Validate setup
fastfold doctor

# List available tools
fastfold tool list

# List loaded skills
fastfold skill list

Interactive commands

Inside fastfold interactive mode:

• /help — command reference + examples
• /tools — list all tools with status
• /agents N <query> — run N parallel research agents
• /sessions, /resume — session lifecycle
• /copy, /export — save/share outputs
• /usage — token and cost tracking

Quick examples

Target prioritization

fastfold "I have a CRBN molecular glue. Proteomics shows it degrades
          IKZF1, GSPT1, and CK1α. Which target should I prioritize?"

Protein folding

fastfold "Fold this sequence with boltz-2 and find the binding pockets: MALWMRLLPLL..."

Combination strategy

fastfold "My lead compound is immune-cold. What combination strategy should I use?"

Key Features

190+ Domain Tools

Category	Examples
Target	Neosubstrate scoring, degron prediction, co-essentiality networks
Chemistry	SAR analysis, fingerprint similarity, scaffold clustering
Expression	L1000 signatures, pathway enrichment, TF activity, immune scoring
Viability	Dose-response modeling, PRISM screening, therapeutic windows
Biomarker	Mutation sensitivity, resistance profiling, dependency validation
Clinical	Indication mapping, population sizing, TCGA stratification
Safety	Anti-target flagging, multi-modal profiling, SALL4 risk
Structure	AlphaFold fetch, docking, binding sites, MD simulation
Folding	Fastfold AI Cloud: boltz-2, monomer, multimer, simplefold_*
Literature	PubMed, OpenAlex, ChEMBL search
DNA	ORF finding, codon optimization, primer design, Gibson/Golden Gate assembly

Agent Skills

Fastfold CLI ships with a bundled skill catalog and supports user-installed skills:

fastfold skill list          # see loaded skills

# Install additional skills (requires npx), check https://skills.sh
npx skills addd <owner/repo>

Data Management

fastfold data pull depmap    # DepMap CRISPR, mutations, expression
fastfold data pull prism     # PRISM cell viability
fastfold data pull msigdb    # Gene sets
fastfold data pull alphafold     # Protein structures (on-demand)

# Or point to existing data
fastfold config set data.depmap /path/to/depmap/

Reports

fastfold report list         # list reports
fastfold report publish      # convert latest .md to .html
fastfold report show         # open in browser

Troubleshooting

Symptom	Fix
fastfold fails at startup	fastfold doctor
No API key	fastfold setup or export ANTHROPIC_API_KEY=...
Data not found	fastfold data pull <dataset>
tiledbsoma / WinError installing [all] on Windows	Prefer WSL2 + Ubuntu and [all] in Linux. Native Windows: [win_build] or [chemistry,biology,ml,analysis] — see Quick install.
Missing dependency (pip fallback)	pip install "fastfold-agent-cli[all]"
ModuleNotFoundError: No module named 'termios' (interactive fastfold on Windows)	Upgrade fastfold-agent-cli ≥ 0.0.36 (e.g. uv tool install "fastfold-agent-cli[win_build]" --python 3.10 --upgrade).
CLINotFoundError / WinError 206 when spawning Claude (Windows)	≥ 0.0.42: run fastfold autofix (or interactive /autofix) and re-run fastfold doctor. This release also avoids oversized Windows CLI command lines by moving large system instructions into the stdin payload path. If still blocked, set shorter UV_TOOL_DIR (uv tools directory) + reinstall, or set FASTFOLD_CLAUDE_CODE_CLI to a known good global Claude Code launcher path.
Session lost	fastfold --continue

Contributing

git clone https://github.com/fastfold-ai/fastfold-agent-cli.git
cd fastfold-agent-cli
uv venv --python 3.12 && uv sync
fastfold setup
pytest tests/

License

MIT — see LICENSE

Credits

Based on CellType CLI