annodex

AI-native bioinformatics workspace by Annoroad, backed by Codex app-server. It provides a browser-native project site, streaming agent chat, branch navigation, docs, and file/result viewing.

Version: 0.1.31 Repository: seqyuan/annodex

Quick Start

npm install -g @seqyuan/annodex
annodex

Open http://localhost:30121 for the project site, or go directly to http://localhost:30121/workspace for the workspace. On first start, annodex can optionally set a password, similar to Jupyter.

CLI

annodex                      # start managed background server
annodex start                # start if not already running
annodex restart              # stop then start
annodex stop                 # stop background server
annodex status               # show server status
annodex logs                 # show recent logs
annodex logs -f              # follow logs
annodex --port 8080          # custom port
annodex --hostname 127.0.0.1 # bind host
annodex --version            # print version
annodex --help               # print help
annodex update               # update global package
annodex passwd               # set/change password
annodex passwd --reset       # remove password

PORT=8080 annodex
ANNODEX_PASSWORD=xxx annodex

Managed servers auto-restart after package updates once active agent sessions are idle. Set ANNODEX_AUTO_RESTART=0 to disable. Legacy ANNOVIBE_* and PIDEX_* environment variables are still accepted for migration.

Data

• Codex threads are read through codex app-server from Codex's own storage.
• annodex settings live under ~/.config/annodex.
• Provider settings are stored in ~/.config/annodex/providers.json.
• Project registry is stored in ~/.config/annodex/annodex-projects.json.
• Password auth is stored in ~/.config/annodex/web-auth.json.

Development

npm install
npm run dev   # port 30121

Typecheck: node_modules/.bin/tsc --noEmit Lint: npm run lint

Do not run next build during dev; it pollutes .next/ and can break npm run dev.