{"_id":"@biomate/connect","name":"@biomate/connect","dist-tags":{"latest":"0.1.0"},"versions":{"0.1.0":{"name":"@biomate/connect","version":"0.1.0","description":"One-line installer that connects BioMate to Claude Code, Claude Desktop, Cursor, Codex, and ChatGPT via OAuth 2.1 + PKCE.","bin":{"biomate-connect":"dist/cli.js"},"main":"./dist/index.js","scripts":{"build":"tsc","test":"vitest run","prepublishOnly":"npm run build"},"keywords":["biomate","mcp","claude","cursor","codex","chatgpt","bioinformatics"],"author":{"name":"BioMate AI"},"license":"MIT","repository":{"type":"git","url":"git+https://github.com/bioMate-AI/biomate-connectors.git","directory":"installer"},"engines":{"node":">=18"},"dependencies":{"keytar":"^7.9.0","open":"^9.1.0"},"devDependencies":{"@types/node":"^20.0.0","typescript":"^5.4.0","vitest":"^1.0.0"},"publishConfig":{"access":"public"},"_id":"@biomate/connect@0.1.0","gitHead":"9d5560530f9eae40f60f3c18e6efd68e3d9dd7e7","types":"./dist/index.d.ts","bugs":{"url":"https://github.com/bioMate-AI/biomate-connectors/issues"},"homepage":"https://github.com/bioMate-AI/biomate-connectors#readme","_nodeVersion":"22.18.0","_npmVersion":"10.9.3","dist":{"integrity":"sha512-weEmVlvBzQc7leNMxFQreAkfQws5heW39XQGl70W+S2sQiBVvbcRpTfcf3Dty5/1b2M9ExOK1wY4CCJ1XffYZA==","shasum":"9207fdc61782e5e8adb40d75750d7c7198652e86","tarball":"https://registry.npmjs.org/@biomate/connect/-/connect-0.1.0.tgz","fileCount":20,"unpackedSize":43597,"signatures":[{"keyid":"SHA256:DhQ8wR5APBvFHLF/+Tc+AYvPOdTpcIDqOhxsBHRwC7U","sig":"MEYCIQC+WirOV73p7PWSFKXOXPteu3BZ0TExTr5Z9mbNp93PZwIhAOuyF2JyzWNPky9WPf5F8HCmpWfJ4P7LOH2sTIvYbpUG"}]},"_npmUser":{"name":"biomate","email":"yaoyun.zhang@biomate.ai"},"directories":{},"maintainers":[{"name":"biomate","email":"yaoyun.zhang@biomate.ai"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages-npm-production","tmp":"tmp/connect_0.1.0_1784652275349_0.057371695226507535"},"_hasShrinkwrap":false}},"time":{"created":"2026-07-21T16:44:35.213Z","0.1.0":"2026-07-21T16:44:35.469Z","modified":"2026-07-21T16:44:35.682Z"},"maintainers":[{"name":"biomate","email":"yaoyun.zhang@biomate.ai"}],"description":"One-line installer that connects BioMate to Claude Code, Claude Desktop, Cursor, Codex, and ChatGPT via OAuth 2.1 + PKCE.","homepage":"https://github.com/bioMate-AI/biomate-connectors#readme","keywords":["biomate","mcp","claude","cursor","codex","chatgpt","bioinformatics"],"repository":{"type":"git","url":"git+https://github.com/bioMate-AI/biomate-connectors.git","directory":"installer"},"author":{"name":"BioMate AI"},"bugs":{"url":"https://github.com/bioMate-AI/biomate-connectors/issues"},"license":"MIT","readme":"# @biomate/connect\n\n> One-line installer that wires BioMate AI into Claude Code, Claude Desktop, Cursor, OpenAI Codex, ChatGPT, and Open Claw (WeChat).\n\nReal bioinformatics — `WGS variant-calling pipeline`, CryoSPARC, AlphaFold, ADMET screens, PBPK — runs from your favorite AI coding assistant. No SaaS lock-in: tokens are stored locally and revocable per-surface from your BioMate account.\n\n## Install\n\n```bash\n# Connect Claude Code\nnpx @biomate/connect claude-code\n\n# Connect Cursor\nnpx @biomate/connect cursor\n\n# Connect Codex CLI\nnpx @biomate/connect codex\n```\n\nThat's it. The CLI opens your browser, runs OAuth 2.1 + PKCE against `https://biomate.ai`, writes the MCP server entry into the right host config file, and stashes a refresh token in your OS keychain.\n\n## Supported surfaces\n\n| Surface | Install command | Config file written |\n|---|---|---|\n| Claude Code | `npx @biomate/connect claude-code` | `~/.claude.json` |\n| Claude Desktop | `npx @biomate/connect claude-desktop` | `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) |\n| Cursor | `npx @biomate/connect cursor` | `~/.cursor/mcp.json` |\n| Codex CLI | `npx @biomate/connect codex` | `~/.codex/config.toml` |\n| ChatGPT | `npx @biomate/connect chatgpt` | (Custom GPT — instructions printed) |\n| Open Claw | `npx @biomate/connect open-claw` | (hosted webhook — account linked) |\n\n## What you get\n\nAfter connecting, your AI assistant has access to BioMate's 14-tool MCP surface:\n\n- **`biomate_session`** — natural-language goal → streaming workflow run with phase/step/QC/findings events\n- **`search_workflow`** + **`get_workflow_spec`** — discover from 2,455 indexed workflows\n- **`run_workflow`** + **`get_run`** + **`cancel_run`** — fine control\n- **`preview_file`**, **`export_report`**, **`recall_memory`**, **`upload_file`**, **`analyze_results`**, **`explain_error`**, **`query_database`**\n\n## Try it\n\nOpen your assistant and paste:\n\n```\nScreen aspirin and caffeine for hERG and CYP3A4 inhibition.\n```\n\n```\nRun RNA-seq differential expression on these FASTQs:\n  s3://biomate-demo/sample_R1.fq.gz, s3://biomate-demo/sample_R2.fq.gz\nCompare treated vs control.\n```\n\n```\nLook up UniProt P04637.\n```\n\n## Privacy & security\n\n- OAuth 2.1 + PKCE; tokens scoped per surface, revocable individually at\n  https://biomate.ai/account/connectors\n- Refresh tokens hashed at rest with HMAC-SHA256\n- Access tokens are 30-minute JWTs; refresh tokens rotate on use (OAuth 2.1 §6.1)\n- No telemetry beyond standard API logs\n\n## Development\n\n```bash\nnpm install\nnpm run build\nnpm test\n```\n\n## License\n\nMIT\n","readmeFilename":"README.md","_rev":"1-d9484380b5bf4156c5e2638288f5ede2"}