Whitehead Claude Code Plugins

A shared plugin marketplace for Claude Code at Whitehead Institute. Plugins provide reusable skills, agents, hooks, and MCP server configurations that extend what Claude Code can do.

Using This Marketplace

Add the marketplace

In any Claude Code session, run:

/plugin marketplace add whitehead/claude-plugins

This registers the marketplace. You only need to do this once — it persists across sessions.

Browse and install plugins

List available plugins:

/plugin search @whitehead

Install a plugin:

/plugin install plugin-name@whitehead

Installed plugins are available immediately. Plugin skills show up as /whitehead:skill-name commands.

Update plugins

Claude Code checks for updates automatically at startup. To update manually:

/plugin marketplace update whitehead

Remove the marketplace

/plugin marketplace remove whitehead

This removes the marketplace and uninstalls its plugins.

Contributing

We welcome contributions from anyone at Whitehead. This marketplace is for shared tools that are broadly useful across the institute. If a plugin is only useful to your personal workflow, keep it in your personal ~/.claude/skills/ directory instead. A good test: "Would someone outside my lab find this useful?"

Naming

Plugin names describe what they do, not where they came from. No lab prefixes, team prefixes, or usernames in plugin names.

Good	Bad
rnaseq-qc	young-lab-rnaseq-qc
demux-pipeline	core-demux
fastq-quality-check	jdoe-qc-helper

Author attribution belongs in plugin.json using the author field, not in the name.

Plugin structure

Each plugin lives in its own directory under plugins/:

plugins/my-plugin/
├── .claude-plugin/
│   └── plugin.json       # Plugin manifest (name, description, version)
└── skills/
    └── my-skill/
        └── SKILL.md       # Skill instructions with YAML frontmatter

A minimal plugin.json:

{
  "name": "my-plugin",
  "description": "What this plugin does",
  "version": "1.0.0"
}

After creating the plugin directory, add an entry to .claude-plugin/marketplace.json:

{
  "name": "my-plugin",
  "source": "my-plugin",
  "description": "What this plugin does"
}

For full plugin authoring docs, see Create plugins.

PR review checklist

This is a public repository on the public internet. Anyone can read it. Before submitting or approving a PR, verify the following:

• No usernames or account names. Do not include MIT Kerberos principals, LDAP usernames, email addresses, GitHub handles, or service account names.
• No real names. Use generic placeholders like your-username or the project maintainer instead of identifying individuals.
• No internal hostnames or paths. Do not reference internal servers, network paths, NFS mounts, or home directory paths (e.g., /home/jdoe/, //fileserver/share).
• No credentials or tokens. No API keys, passwords, certificates, or secrets of any kind — even examples that look fake could be real.
• No internal URLs. Do not include links to intranet sites, internal wikis, Jira/Confluence instances, or other systems not accessible to the public.
• No institutional operational details. Avoid references to specific lab names, internal project codenames, or infrastructure details that are not already public.

If a skill needs to reference user-specific values (paths, usernames, endpoints), use environment variables or clearly marked placeholders that each user fills in locally.

Development workflow

1. Fork or branch from master.
2. Create your plugin under plugins/.
3. Add the marketplace entry in .claude-plugin/marketplace.json.
4. Test locally:

   claude --plugin-dir ./plugins/my-plugin
   

5. Open a PR. Another team member reviews using the checklist above.