{"id":46453298,"url":"https://github.com/elnora-ai/elnora-cli","last_synced_at":"2026-05-26T00:00:58.942Z","repository":{"id":342305773,"uuid":"1173195885","full_name":"Elnora-AI/elnora-cli","owner":"Elnora-AI","description":"Elnora CLI — command-line interface for the Elnora bioprotocol platform","archived":false,"fork":false,"pushed_at":"2026-05-22T17:09:01.000Z","size":562,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-22T21:27:04.151Z","etag":null,"topics":["biotech","claude-code-plugin","cli","elnora","protocol-generation","python"],"latest_commit_sha":null,"homepage":"https://elnora.ai","language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Elnora-AI.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":".github/SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-03-05T05:22:46.000Z","updated_at":"2026-05-22T17:06:44.000Z","dependencies_parsed_at":"2026-05-26T00:00:42.477Z","dependency_job_id":null,"html_url":"https://github.com/Elnora-AI/elnora-cli","commit_stats":null,"previous_names":["elnora-ai/elnora-cli"],"tags_count":36,"template":false,"template_full_name":null,"purl":"pkg:github/Elnora-AI/elnora-cli","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Elnora-AI%2Felnora-cli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Elnora-AI%2Felnora-cli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Elnora-AI%2Felnora-cli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Elnora-AI%2Felnora-cli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Elnora-AI","download_url":"https://codeload.github.com/Elnora-AI/elnora-cli/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Elnora-AI%2Felnora-cli/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33497930,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-25T14:31:05.219Z","status":"ssl_error","status_checked_at":"2026-05-25T14:31:02.878Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biotech","claude-code-plugin","cli","elnora","protocol-generation","python"],"created_at":"2026-03-06T01:00:35.223Z","updated_at":"2026-05-26T00:00:58.898Z","avatar_url":"https://github.com/Elnora-AI.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Elnora CLI\n\nCommand-line interface for the [Elnora AI Platform](https://platform.elnora.ai).\n\n[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)\n[![npm](https://img.shields.io/npm/v/@elnora-ai/cli)](https://www.npmjs.com/package/@elnora-ai/cli)\n\n[Elnora](https://elnora.ai) is an AI agent for biotech and pharma teams that generates, optimizes, and troubleshoots preclinical lab protocols. She learns from both successful and failed experiments, building knowledge that compounds with every project.\n\nThe CLI gives you full access to the platform from your terminal — collaborate with the agent, manage protocols and files, and integrate Elnora into your automation pipelines.\n\n## What You Can Do\n\n- **Generate and optimize protocols** — from iPSC differentiation to assay development, with citations from 36M+ PubMed articles and preprint servers\n- **Access 2,100+ scientific tools** — protein structure prediction (AlphaFold3), molecular cloning design, glycan analysis, drug-target databases (ChEMBL, UniProt, Open Targets), and more\n- **Stream agent responses in real-time** — pipe structured output directly into your scripts and workflows\n- **Manage projects and files with version control** — track protocol iterations, fork and promote versions, search across your entire knowledge base\n- **Run as an MCP server** — plug Elnora into Claude Code, Cursor, or any MCP-compatible AI tool as a first-class integration\n\n## Requirements\n\n- macOS, Linux, or Windows\n- Node.js 20+ (npm install only — not required for curl/Homebrew)\n- An Elnora API key — [get one here](https://platform.elnora.ai)\n\n## Install\n\n```bash\n# macOS / Linux\ncurl -fsSL https://cli.elnora.ai/install.sh | bash\n\n# Windows (PowerShell)\nirm https://cli.elnora.ai/install.ps1 | iex\n\n# npm (requires Node.js 20+)\nnpm install -g @elnora-ai/cli\n\n# Homebrew\nbrew install elnora-ai/cli/elnora\n```\n\n## Skills \u0026 Setup\n\nAfter installing the CLI, configure your AI coding tools:\n\n```bash\nelnora setup\n```\n\nThis auto-detects which tools you have installed and configures them:\n\n- **Claude Code** — registers the `elnora-plugins` marketplace and enables 9 skills (`elnora-tasks`, `elnora-projects`, `elnora-files`, etc.) so you can use natural language.\n- **Cursor / VS Code / Codex** — writes an MCP server config pointing at `https://mcp.elnora.ai/mcp` with your API key.\n\nTarget a specific tool: `elnora setup claude` · `elnora setup cursor` · `elnora setup vscode` · `elnora setup codex`.\n\n### What You Get in Claude Code\n\nOnce configured, restart Claude Code and try any natural-language request:\n\n\u003e \"Use Elnora to generate a PCR protocol for BRCA1 exon 11\"\n\u003e \"Use Elnora to list my projects\"\n\u003e \"Use Elnora to optimize the protocol in task abc-123\"\n\nClaude will invoke the `elnora` CLI under the hood using the bundled skills. No need to memorize command syntax.\n\n### Where Everything Lives\n\n| What | Where |\n|------|-------|\n| CLI binary (macOS/Linux) | `~/.local/bin/elnora` |\n| CLI binary (Windows) | `%USERPROFILE%\\.elnora\\bin\\elnora.exe` |\n| Auth / profiles | `~/.elnora/profiles.toml` (mode 0600) |\n| Claude Code skills | `~/.claude/plugins/marketplaces/elnora-plugins/elnora/skills/` (auto-updated) |\n| Claude Code settings | `~/.claude/settings.json` — look for `elnora@elnora-plugins: true` |\n\n### Manual Plugin Setup\n\nIf `elnora setup claude` doesn't work for some reason, you can install the plugin manually:\n\n1. In Claude Code, run `/plugin`\n2. Choose \"Add marketplace\"\n3. Enter: `Elnora-AI/elnora-plugins`\n4. Run `/plugin` again → Plugins → Enable `elnora`\n\n## Quick Start\n\n```bash\nelnora auth login\nelnora projects list\nelnora tasks create --project \u003cid\u003e --message \"Analyze kinase inhibitors\"\nelnora tasks send \u003ctask-id\u003e --message \"Focus on selectivity\" --stream\n```\n\n## Commands\n\n| Group | Commands |\n|-------|----------|\n| `auth` | login, logout, status, profiles, validate |\n| `projects` | list, get, create, update, archive, members, add-member, update-role, remove-member, leave |\n| `tasks` | list, get, create, send (--stream, --wait), messages, update, archive |\n| `files` | list, get, content, create, upload, download, update, archive, versions, fork, promote, working-copy, commit |\n| `orgs` | list, get, create, update, members, billing, invite, invitations, resend-invite, cancel-invite, delete |\n| `folders` | list, create, rename, move, delete |\n| `search` | tasks, files, all, file-content |\n| `library` | files, folders, create-folder, rename-folder, delete-folder |\n| `account` | get, update, agreements, accept-terms, delete, users |\n| `api-keys` | create, list, revoke, get-policy, set-policy |\n| `audit` | list |\n| `feedback` | submit |\n| `flags` | list, get, set |\n| `health` | check |\n\n### Utility Commands\n\n```bash\nelnora doctor              # Check API, auth, version, config\nelnora whoami              # Show current profile and org\nelnora open [page]         # Open platform in browser (docs, keys, billing)\nelnora completion \u003cshell\u003e  # Generate shell completions (bash, zsh, fish)\nelnora mcp serve           # Start built-in MCP server\n```\n\n## Streaming\n\nReal-time agent responses directly in your terminal:\n\n```bash\n# Stream agent output as it generates\nelnora tasks send \u003ctask-id\u003e --message \"Optimize this protocol\" --stream\n\n# Wait for the complete response (polling)\nelnora tasks send \u003ctask-id\u003e --message \"Optimize this protocol\" --wait\n```\n\nStatus output (thinking, tool calls) goes to stderr. Content goes to stdout, so streaming is pipeable:\n\n```bash\nelnora tasks send \u003ctask-id\u003e --message \"Analyze this\" --stream \u003e response.txt\n```\n\n## MCP Server\n\nThe CLI includes a built-in MCP server that exposes all commands as tools:\n\n```bash\n# Start HTTP MCP server (for deployment)\nelnora mcp serve --http\n\n# Start stdio MCP server (for local MCP clients)\nelnora mcp serve --stdio\n```\n\nConfigure in Claude Code or Cursor:\n\n```json\n{\n  \"elnora\": {\n    \"type\": \"http\",\n    \"url\": \"https://mcp.elnora.ai/mcp\"\n  }\n}\n```\n\n## Authentication\n\n```bash\n# Login with API key\nelnora auth login\n\n# Multi-org profiles\nelnora auth login --profile university\nelnora --profile university projects list\n\n# Check status\nelnora doctor\n```\n\nAPI keys are stored in `~/.elnora/profiles.toml` with secure file permissions (0600).\n\n## Output Formats\n\n```bash\nelnora projects list                    # JSON (default)\nelnora projects list --compact          # Compact JSON\nelnora projects list --output csv       # CSV\nelnora projects list --fields id,name   # Field filtering\nelnora projects list --json             # Force JSON (even in TTY)\n```\n\n## Documentation\n\n- [Migration Guide](MIGRATION.md) — migrating from the Python CLI\n- [API Reference](https://docs.elnora.ai)\n- [Platform](https://platform.elnora.ai)\n\n## License\n\nApache-2.0\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felnora-ai%2Felnora-cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Felnora-ai%2Felnora-cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felnora-ai%2Felnora-cli/lists"}