Install

npm install -g @ivybiosciences/ivybloom-cli    # npm
npx @ivybiosciences/ivybloom-cli [command]     # run without install
brew install ivybiosciences/ivybloom/ivybloom  # macOS/Linux

Verify: ivybloom --version

Quick Start

ivybloom auth login     # authenticate (opens browser)
ivybloom tui            # launch interactive TUI
ivybloom tools list     # list available tools

Tools

| Tool | Description | Input | |------|-------------|-------| | ESMFold | Fast protein structure prediction (single sequence) | FASTA/sequence | | AlphaFold | High-accuracy structure prediction (MSA-based) | FASTA | | DiffDock | Molecular docking with diffusion models | PDB + SMILES/SDF | | REINVENT | De novo drug molecule generation | SMILES scaffold | | ADMET | Absorption, distribution, metabolism, excretion, toxicity | SMILES | | MolMIM | Molecular property prediction | SMILES | | ProteinMPNN | Inverse folding / sequence design | PDB | | RFdiffusion | Protein structure generation | Constraints |

Run tools via CLI or TUI with real-time progress streaming.

CLI Reference

# Authentication
ivybloom auth login [--browser|--token]
ivybloom auth logout
ivybloom auth status

# Tools
ivybloom tools list [--format json|table]
ivybloom tools info <tool>
ivybloom tools run <tool> [--input FILE] [--param KEY=VAL...]

# Jobs
ivybloom jobs list [--status pending|running|completed|failed] [--limit N]
ivybloom jobs status <job-id>
ivybloom jobs logs <job-id> [--follow]
ivybloom jobs cancel <job-id>
ivybloom jobs download <job-id> [--output DIR]

# Projects
ivybloom projects list
ivybloom projects create <name>
ivybloom projects link <project-id>
ivybloom projects unlink

# Sessions (agent harness)
ivybloom sessions list
ivybloom sessions resume <session-id>
ivybloom checkpoints list <session-id>
ivybloom checkpoints rollback <session-id> <checkpoint-id>

# Utilities
ivybloom config [get|set|list]
ivybloom version [--verbose]
ivybloom doctor                    # diagnose environment issues

TUI

Launch: ivybloom tui

Keyboard Shortcuts

| Key | Action | |-----|--------| | @ | Attach file (FASTA, PDB, SDF, SMILES) | | ! | Browse & run tools | | / | Command palette | | y/n | Approve/deny tool execution | | Tab | Toggle context panel | | Ctrl+J | Submit message | | Ctrl+C | Cancel/exit | | ? | Help |

Features

• AI Chat: Conversational interface for research guidance and tool selection
• Tool Approval: Review parameters before execution (Cursor-style flow)
• Live Progress: Real-time job status with phase indicators
• File Attachments: Drag-drop or @-mention to attach sequences/structures
• Session Persistence: Resume conversations with full context

Automation & CI/CD

Enable machine-readable JSON output for scripting:

ivybloom jobs list --machine                    # JSON envelope output
IVYBLOOM_MACHINE_MODE=1 ivybloom tools run ...  # via env var
ivybloom jobs status <id> --machine --trace-id "run-001"

Output format:

{"success": true, "data": {...}, "meta": {"trace_id": "...", "duration_ms": 42}}

Environment Variables

| Variable | Description | |----------|-------------| | IVYBLOOM_API_KEY | API key (for CI/CD, skips interactive login) | | IVYBLOOM_API_URL | Override API endpoint | | IVYBLOOM_MACHINE_MODE=1 | JSON output, no colors/prompts | | IVYBLOOM_DEBUG=1 | Verbose debug output | | IVYBLOOM_DISABLE_KEYRING=1 | Store tokens in file instead of OS keychain | | DO_NOT_TRACK=1 | Disable install telemetry | | IVYBLOOM_NO_TELEMETRY=1 | Disable install telemetry (alias) |

Telemetry

The installer sends anonymous telemetry to help us understand usage patterns. Data collected: platform, architecture, version, CI detection, success/failure. No PII is collected. Disable with DO_NOT_TRACK=1 or IVYBLOOM_NO_TELEMETRY=1.

Platform Support

| OS | Architectures | |----|---------------| | macOS | x64, arm64 (Apple Silicon) | | Linux | x64, arm64 | | Windows | x64 |

Troubleshooting

| Issue | Solution | |-------|----------| | 401 Unauthorized | Run ivybloom auth login --browser | | Token errors | Set IVYBLOOM_DISABLE_KEYRING=1 | | Connection timeout | Check IVYBLOOM_API_URL or network | | TUI rendering issues | Ensure terminal supports 256 colors |

Run ivybloom doctor for automated diagnostics.