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    Ivy Biosciences Docs/Call the platform/Cli/ivybloom CLI Commands — Complete Reference

    ivybloom CLI Commands — Complete Reference

    Reference for every ivybloom CLI command and its MCP equivalent, organized by category with flags and parameter formats.

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    commandsreferencecliapi

    This reference lists every ivybloom CLI command — CLI subcommands plus their MCP tools — organized by category so you can build reproducible, scriptable pipelines. Reach for it when you need exact flags, parameter formats, or the MCP equivalents for a command while wiring up batch jobs or CI/CD. Because the CLI shares one backend and job history with the web platform, any command here operates on the same data as your web work. For a guided starting point, see the CLI overview.

    Difficulty

    intermediate

    Commands Reference

    Complete reference for all ivybloom CLI commands organized by category. CLI subcommands plus MCP tools.

    Commands marked with MCP are available via ivybloom mcp serve for AI agent integration and do not have dedicated CLI subcommands. See MCP Integration for the full tool catalog.

    Authentication

    Manage authentication and account access. See API Keys & Authentication for detailed documentation.

    Job Submission

    Submit computational jobs using the run command. See Job Management for monitoring and results.

    Job Management

    Monitor and manage computational jobs. See Job Management for full documentation.

    Computational Tools

    Browse and inspect available tools.

    Batch Processing

    Submit and manage parallel job collections. See Batch Processing for full documentation.

    batch is a hidden command — accessible directly but not shown in default --help.

    Compounds

    Manage molecular compound collections. See Compounds for full documentation.

    Protein Preparation

    Prepare protein structures for docking. See Protein Preparation for full documentation.

    Projects

    Sync

    Synchronize project data between local and remote.

    Orchestration

    Natural language job submission. See Orchestration for full documentation.

    MCP Server

    Model Context Protocol server for AI agents. See MCP Integration for full documentation.

    Sessions & Checkpoints

    Persistent conversations with time-travel. See Sessions & Checkpoints for full documentation.

    Chats

    Benchmarking

    AI Completions

    Campaigns

    Workflows & Templates

    Account & Profile

    Billing & Credits

    See Billing & Credits for full documentation.

    Organizations

    See Organizations for full documentation.

    API Keys

    Devices

    Alerts & Notifications

    Data Management

    Exports & Reports

    Feature Flags

    Interactive Modes

    Utilities

    Configuration

    Manage CLI settings. See Configuration for full documentation.

    Global Options

    These options work with any command:

    OptionShortDefaultDescription
    --help-h—Show help for command
    --version-v—Show CLI version
    --profile <name>—"default"Use a specific configuration profile
    --debug—falseEnable debug output
    --trace—falseEnable trace-level logging
    --trace-id <id>——Set request correlation ID
    --format <fmt>—from configOutput format (table, json, csv, yaml)
    --output-format <fmt>—from configAlias for --format
    --json—falseShorthand for --format json
    --no-color—falseDisable colored output
    --dry-run—falseValidate without executing
    --script—falseScript mode: no TUI, no spinners
    --agent—falseAgent mode: structured JSON envelope
    --campaign-c—Scope operations to a campaign
    --message-m—Send a single headless message
    --continue——Continue a chat by ID or "last"
    --resume-r—Alias for --continue
    --force—falseApply changes without confirmation
    --apply—falseApply file changes (safer than --force)
    --follow—falseWait for job/batch completion
    --stream-partial-output—falseStream text deltas

    For CI/CD automation, use --agent for structured JSON output or --script for non-interactive mode. See Agent Mode for details.

    Environment Variables

    VariableDescription
    IVYBLOOM_API_KEYAPI key for authentication
    IVYBLOOM_API_URLOverride API base URL
    IVYBLOOM_DEBUG=1Enable debug output
    NO_COLOR=1Disable colored output
    IVYBLOOM_AGENT_MODE=1Enable agent JSON output
    IVYBLOOM_SCRIPT_MODE=1Enable script-friendly output
    IVYBLOOM_TRACE_IDRequest correlation ID
    IVYBLOOM_TEST_MODE=1Enable test mode
    IVYBLOOM_MOCK_MODE=1Enable mock responses
    # Use API key from environment (CI/CD)
export IVYBLOOM_API_KEY="ivy_yourKeyId_yourSecret"
ivybloom jobs list --format json

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    Campaigns & Workspace Organization

    Organize drug discovery projects with campaigns that group related chats, jobs, and results.

    Compound Collections

    Create, search, import, and export molecular compound libraries from the command line.

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