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skill basic
drorhilman Apr 22, 2026
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drorhilman Apr 22, 2026
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# skills
Code Ocean skills
# Code Ocean Skills

Skills for AI coding agents to interact with the [Code Ocean](https://codeocean.com) computational research platform.

## Available Skills

### `codeocean`

Teaches AI agents how to use the Code Ocean API through three access methods:

- **MCP Server** (26 tools) — primary interface for AI agents
- **Python SDK** (`codeocean` package) — for writing Python scripts
- **REST API** (curl/wget) — for shell commands and manual API calls

Covers capsules, pipelines, computations, data assets, custom metadata, authentication, permissions, search, and pagination.

## Prerequisites

1. A Code Ocean account with API access
2. An API access token (generated from Account > Access Tokens)
3. One or more of:
- The Code Ocean MCP server (`codeocean-mcp-server`) for agent-based interaction
- The Python SDK (`pip install codeocean`) for programmatic access
- `curl` for direct REST API calls

## Quick Start

### 1. Generate an API Token

1. Sign into your Code Ocean instance
2. Go to **Account > Access Tokens > Generate New Token**
3. Select scopes (Capsule Read/Write, Datasets Read/Write)
4. Copy the token immediately — it is only shown once

### 2. Install the MCP Server (for AI agents)

Install `uv` and Python 3.10+, then configure your agent. Example for Claude Desktop:

```json
{
"mcpServers": {
"codeocean": {
"command": "uvx",
"args": ["codeocean-mcp-server"],
"env": {
"CODEOCEAN_DOMAIN": "https://your-instance.codeocean.com",
"CODEOCEAN_TOKEN": "<YOUR_TOKEN>",
"AGENT_ID": "Claude Desktop"
}
}
}
}
```

See `codeocean/references/mcp-server-install.md` for configs for VS Code, Cline, Roo Code, Cursor, and Windsurf.

### 3. Install the Skill

- This skill lives in the [`codeocean/skills`](https://github.com/codeocean/skills) repository.
- The skill folder is at [`<skill-path-in-repo>`](https://github.com/codeocean/skills/tree/main/<skill-path-in-repo>). The entry point is `SKILL.md`.
- **Install the entire skill folder**, not just `SKILL.md` — supporting files (references, templates, examples) are referenced by the entry point.
- The fastest cross-agent option is [`gh skill`](#github-cli-universal-installer) if available.

| Agent | Install method | Exact path / command | Notes |
| ----------------------------------- | ------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **Claude Code** | Manual folder copy | Project: `.claude/skills/<skill-name>/`<br>User: `~/.claude/skills/<skill-name>/`<br>Plugin: `<plugin>/skills/<skill-name>/` | Copy full folder from [`<skill-path-in-repo>`](https://github.com/codeocean/skills/tree/main/<skill-path-in-repo>). Claude watches these directories automatically. |
| **Codex** | A. Manual folder copy<br>B. Plugin install | A. `$CWD/.agents/skills/<skill-name>/`<br>`$REPO_ROOT/.agents/skills/<skill-name>/`<br>`$HOME/.agents/skills/<skill-name>/`<br>`/etc/codex/skills/<skill-name>/`<br>B. In-app: add from plugin directory<br>CLI: `/plugins` → Install plugin | Clone/download from `codeocean/skills`, copy the folder at `<skill-path-in-repo>`. Codex supports skills natively; packaged distribution is often via plugins. |
| **Cursor** | Plugin-first | Install plugin from marketplace / team marketplace | No official direct raw GitHub skill install documented. Use `gh skill` row below for GitHub-based install. |
| **OpenCode** | Manual folder copy | `.opencode/skills/<skill-name>/`<br>`~/.config/opencode/skills/<skill-name>/`<br>Also compatible:<br>`.claude/skills/<skill-name>/`<br>`~/.claude/skills/<skill-name>/`<br>`.agents/skills/<skill-name>/`<br>`~/.agents/skills/<skill-name>/` | Copy full folder from [`<skill-path-in-repo>`](https://github.com/codeocean/skills/tree/main/<skill-path-in-repo>). |
| **Antigravity** | Manual folder copy | `.agents/skills/<skill-name>/`<br>`~/.gemini/antigravity/skills/<skill-name>/` | Defaults to `.agents/skills`. Copy full folder. |
| **Windsurf** | Manual folder copy | `.windsurf/skills/<skill-name>/`<br>`~/.codeium/windsurf/skills/<skill-name>/`<br>Enterprise: macOS `/Library/Application Support/Windsurf/skills/`, Linux/WSL `/etc/windsurf/skills/`, Windows `C:\ProgramData\Windsurf\skills\` | Each skill is a subdirectory containing `SKILL.md`. Copy full folder. |
| **GitHub Copilot CLI** | Manual folder copy | Project: `.github/skills/<skill-name>/`, `.claude/skills/<skill-name>/`, `.agents/skills/<skill-name>/`<br>Personal: `~/.copilot/skills/<skill-name>/`, `~/.claude/skills/<skill-name>/`, `~/.agents/skills/<skill-name>/` | Clone/download from `codeocean/skills`, copy the full folder at `<skill-path-in-repo>`. |
| **VS Code / Copilot agent plugins** | Plugin from Git source | Run `Chat: Install Plugin From Source` → enter Git repo URL | This is for **plugins**, not raw skill folders. Applies only if the skill is wrapped as a plugin. Does not apply to raw skill repos like `codeocean/skills`. |
| **Gemini CLI** | Native GitHub install | `gemini skills install https://github.com/codeocean/skills.git --path <skill-path-in-repo>`<br>`gemini skills install /path/to/local/<skill-name> --scope workspace`<br>`gemini skills link /path/to/local/<skill-name> --scope workspace` | Supports Git repo, local dir, zipped `.skill`, monorepo subpath, workspace/user scope. Use `--path` for monorepo subpath. |
| **Cline** | Manual folder copy | `.cline/skills/<skill-name>/`<br>`~/.cline/skills/<skill-name>/` | Enable Skills in Settings → Features → Enable Skills. Experimental. |
| **Kiro IDE** | Native GitHub import | Agent Steering & Skills → `+` → Import a skill → GitHub → paste `https://github.com/codeocean/skills/tree/main/<skill-path-in-repo>` | URL must point to the subdirectory, not the repo root. Imported skills are copied into the skills directory. |
| **Kiro CLI** | Manual folder copy | `.kiro/skills/<skill-name>/`<br>`~/.kiro/skills/<skill-name>/` | Default agent auto-loads skills. Custom agents need `skill://` resources configured. |
| **`gh skill` (GitHub CLI)** | Universal GitHub install | `gh skill install codeocean/skills <skill-name>`<br>`gh skill install codeocean/skills <skill-name> --agent claude-code`<br>`gh skill install codeocean/skills <skill-name> --agent cursor`<br>`gh skill install codeocean/skills <skill-name> --agent codex`<br>`gh skill install codeocean/skills <skill-name> --agent gemini`<br>`gh skill install codeocean/skills <skill-name> --agent antigravity` | Installs to the correct host directory automatically. Can pin versions/commits. Cleanest cross-agent GitHub-hosted option. |

#### Shared patterns

- **Manual folder copy**: Claude Code, Codex, OpenCode, Antigravity, Windsurf, GitHub Copilot CLI, Cline, Kiro CLI — copy the skill directory (containing `SKILL.md` and supporting files) into the agent's watched skills path.
- **Native GitHub import/install**: Gemini CLI (`gemini skills install`), Kiro IDE (GitHub import UI) — install directly from `codeocean/skills` repo.
- **Plugin-first**: Cursor, VS Code / Copilot agent plugins — skill distribution is via marketplace or Git-source plugins, not raw skill folders.
- **Universal GitHub installer**: `gh skill install codeocean/skills <skill-name>` — routes to the correct agent directory automatically; works across Claude Code, Codex, Cursor, Gemini, Antigravity.

#### References

- [Claude Code — Skills](https://code.claude.com/docs/en/skills)
- [Codex — Skills](https://developers.openai.com/codex/skills)
- [Codex — Plugins](https://developers.openai.com/codex/plugins)
- [OpenCode — Skills](https://opencode.ai/docs/skills)
- [Antigravity — Skills](https://antigravity.google/docs/skills)
- [Windsurf — Skills](https://docs.windsurf.com/windsurf/cascade/skills)
- [GitHub Copilot CLI — Skills](https://docs.github.com/en/copilot/how-tos/copilot-cli/customize-copilot/add-skills)
- [VS Code — Agent plugins](https://code.visualstudio.com/docs/copilot/customization/agent-plugins)
- [Gemini CLI — Skills](https://geminicli.com/docs/cli/skills/)
- [Cline — Skills](https://docs.cline.bot/customization/skills)
- [Kiro IDE — Skills](https://kiro.dev/docs/skills/)
- [Kiro CLI — Skills](https://kiro.dev/docs/cli/skills/)
- [`gh skill` — GitHub CLI](https://github.blog/changelog/2026-04-16-manage-agent-skills-with-github-cli/)

## Skill Structure

```
codeocean/
├── SKILL.md # Main skill — workflows, decision tree, concepts
└── references/
├── mcp-guide.md # MCP workflow patterns and anti-patterns
├── mcp-tools-catalog.md # All 26 MCP tools with parameter schemas
├── mcp-server-install.md # Install configs for 6 editors/agents
├── cli-guide.md # curl/wget endpoint reference
├── sdk-guide.md # Python SDK setup and examples
├── setup-and-auth.md # Token generation and environment variables
├── capsules.md # Capsule data model and operations
├── pipelines.md # Pipeline-specific operations
├── computations.md # Running, waiting, result retrieval
├── data-assets.md # Data asset creation and lifecycle
├── custom-metadata.md # Admin-defined metadata schema
├── search-and-pagination.md # Query syntax and pagination
└── permissions.md # User/group access control
```

## How It Works

The skill uses **progressive disclosure**:

1. **SKILL.md** loads when the skill triggers — contains workflow patterns and a decision tree
2. **Reference files** load on demand — agents only read the files relevant to their current task

This keeps context window usage efficient while providing deep coverage of the entire Code Ocean API.

## Links

- [Code Ocean User Guide](https://docs.codeocean.com/user-guide) — platform documentation
- [Code Ocean API Documentation](https://docs.codeocean.com/user-guide/code-ocean-api) — REST API reference
- [Code Ocean Python SDK](https://github.com/codeocean/codeocean-sdk-python) — GitHub repo
- [Code Ocean MCP Server](https://github.com/codeocean/codeocean-mcp-server) — GitHub repo
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