JupyterLite + Galaxy Integration

This project integrates JupyterLite with the Pyodide kernel and custom extensions such as jl-galaxy.

The jl-galaxy extension enables Jupyter users to interact seamlessly with their Galaxy history — including loading and saving notebooks — through a fully integrated browser-based interface.

⚙️ Requirements

- Python 3.10.17+
- Node.js 20.19.1+
- npm 10.8.2+

---

📦 Setup Instructions

$3

``bash
python -m venv .venv
source .venv/bin/activate
`

$3

`bash
pip install -r requirements.txt
`

This installs jupyterlite, jupyterlite-pyodide-kernel, and the gxy utility module for Galaxy integration.

$3

`bash
npm install
`

This installs JavaScript dependencies listed in package.json, including custom JupyterLite extensions.

---

🔨 Build

Run the full build to generate a standalone JupyterLite distribution:

`bash
npm run build
`

This will:
- Run jupyter lite build
- Include the Pyodide kernel
- Bundle federated extensions like jl-galaxy
- Output the final static site to: ./static/dist/_output

---

🚀 Serve

To serve the JupyterLite site locally:

`bash
npm run serve
`

Then open http://localhost:3000 in your browser.

---

🧰 Galaxy Integration Utilities (gxy)

The gxy module provides Python functions to interact with the Galaxy API directly from JupyterLite.

$3

Makes an HTTP request to a Galaxy API endpoint and returns the parsed JSON response.

`python
await api("/api/histories")
await api("/api/histories", method="POST", data={"name": "New History"})
`

---

$3

Downloads dataset(s) by HID, ID, or regex pattern. Saves them to Pyodide's virtual filesystem.

`python
await get(3) # by HID
await get("some_id", "id")
await get("myfile.*", "regex")
await get("mytag", "tag")
`

---

$3

Uploads a file from the virtual filesystem to the current Galaxy history.

`python
await put("mydata.txt", "newname.txt", ext="txt")
`

---

$3

Returns metadata for all visible datasets in the current history.

`python
await get_history()
`

---

$3

Returns the current history ID based on the dataset context.

`python
await get_history_id()
`

---

$3


Returns the Galaxy environment injected into the session via __gxy__.

`python
get_environment()
`

---

$3

Used internally to resolve regex patterns to dataset identifiers.

---

📎 Notes

- The jl-galaxy extension allows users to browse and manage Galaxy histories directly from the Jupyter UI.
- All files must be placed within static/dist/_output; writing outside this directory breaks the build.
- The upload helper uses XMLHttpRequest to work around Pyodide's limitations with fetch`.