open-index/open-npm huggingface dataset:
npm package: @galaxyproject/aequatus
Description: Authors: --------
Latest version: 0.0.0

Authors:
--------

<a href="https://github.com/anilthanki">Anil Thanki</a>, <a href="https://github.com/nsoranzo">Nicola Soranzo</a> and <a href="https://github.com/froggleston">Rob Davey</a>.


Citation:
---------
If you are using Aequatus for any kind of research purpose, please cite:

Thanki AS, Soranzo S, Herrero J, Haerty W. Davey RP. Aequatus: An open-source homology browser. GigaScience 2018; doi: [10.1093/gigascience/giy128]( https://doi.org/10.1093/gigascience/giy128)
npm package: @galaxyproject/alignmentviewer
Description: This repository provides a Galaxy visualization plugin for **Sequence Alignment Viewer 2.0**, built directly from the official GitHub source code.
Author: Nicholas Gauthier
Latest version: 0.0.3

# Galaxy Visualization: Alignment Viewer

This repository provides a Galaxy visualization plugin for **Sequence Alignment Viewer 2.0**, built directly from the official GitHub source code.

## Overview

The visualization integrates the Sequence Alignment Viewer into the Galaxy platform, allowing users to explore sequence alignments interactively within Galaxy workflows.

## Notes on Build

The published **npm package** and the corresponding example provided by the original group did not build successfully in this environment due to reliance on **expected global variables** that were not defined at runtime.  

To work around this, the visualization was rebuilt directly from the GitHub source, using a custom Webpack configuration to correctly provide globals and to package the assets in a form usable by Galaxy.

## Build

Install dependencies and build the visualization assets:

```bash
yarn install
yarn build
npm package: @galaxyproject/cytoscape
Description: This project is a Galaxy visualization package that integrates [Cytoscape](https://cytoscape.org/) into the Galaxy platform using the [Galaxy Charts](https://galaxyproject.github.io/galaxy-charts/) and [Cytoscape package](https://www.npmjs.com/package/@ga
Author: Alireza Heidari
Latest version: 0.0.8

# Galaxy Visualization Tool: Cytoscape

This project is a Galaxy visualization package that integrates [Cytoscape](https://cytoscape.org/) into the Galaxy platform using the [Galaxy Charts](https://galaxyproject.github.io/galaxy-charts/) and [Cytoscape package](https://www.npmjs.com/package/@galaxyproject/cytoscape).

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins.

## Development

To run the development server, use the following commands:

```bash
npm install
npm run dev
```

## Production

To build the production version, use the following command:

```bash
npm run build
```

## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
npm package: @galaxyproject/gx-it-proxy
Description: A dynamic reverse proxy for Interactive Tools in Galaxy
Author: Galaxy Project
Latest version: 0.2.3

# A dynamic configurable reverse proxy for use within Galaxy

## Invoking

This project can be invoked from ``lib/main.js`` script in the source or
installed and invoked through its [published package](https://www.npmjs.com/package/@galaxyproject/gx-it-proxy) via npm or npx.

```console
$ npx @galaxyproject/gx-it-proxy --version
$ npx @galaxyproject/gx-it-proxy --sessions test.sqlite --port 8001  # use SQLite
$ npx @galaxyproject/gx-it-proxy --sessions test.json --port 8001    # use a JSON file
$ npx @galaxyproject/gx-it-proxy --sessions postgresql:///galaxy?host=/var/run/postgresql --port 8001  # use PostgreSQL
```

## Double Proxy

To double-proxy (e.g. from Galaxy to a remote proxy that proxies to the application):

```console
host1$ ./lib/main.js --sessions test.sqlite --forwardIP host2 --forwardPort 8001
host2$ ./lib/main.js --port 8001
```

## Sessions

The proxy loads sessions from the file or database passed with the `--sessions`
option. SQLite and JSON files are watched and reloaded on every change.
PostgreSQL databases are polled every five seconds by default. The polling
interval can be configured via the `--pollingInterval` option (in ms).

Faster updates for PostgreSQL databases are possible via
[PostgreSQL asynchronous notifications](https://www.postgresql.org/docs/16/libpq-notify.html).
To enable them, create a PostgreSQL trigger that sends a
NOTIFY message to the channel `gxitproxy` every time the table `gxitproxy`
changes. 

```SQL
CREATE OR REPLACE FUNCTION notify_gxitproxy()
RETURNS trigger AS $$
BEGIN
  PERFORM pg_notify('gxitproxy', 'Table "gxitproxy" changed');
  RETURN NEW;
END;
$$ LANGUAGE plpgsql;

CREATE TRIGGER gxitproxy_notify
AFTER INSERT OR UPDATE OR DELETE ON gxitproxy
FOR EACH ROW EXECUTE FUNCTION notify_gxitproxy();
```

Although it is possible to disable polling using `--pollingInterval 0`, it is
strongly discouraged, as the delivery of asynchronous notifications is not
guaranteed.
npm package: @galaxyproject/hivtrace
Description: The HIV-Trace Viewer is a Galaxy visualization plugin for interactive exploration of transmission networks inferred by **HIV-TRACE**. It renders graph-based results directly inside Galaxy, allowing users to examine connected components, cluster sizes, and
Latest version: 0.0.1

# HIV-Trace Viewer (Galaxy Plugin)

The HIV-Trace Viewer is a Galaxy visualization plugin for interactive exploration of transmission networks inferred by **HIV-TRACE**. It renders graph-based results directly inside Galaxy, allowing users to examine connected components, cluster sizes, and metadata-linked attributes.

## Features
- Network visualization of HIV-TRACE output
- Interactive node and edge exploration
- Metadata integration for coloring and filtering
- Seamless embedding into the Galaxy visualization framework

## Installation
Place the plugin directory under Galaxy’s `config/plugins/visualizations/` and restart Galaxy.

## Usage
1. Run **HIV-TRACE** within Galaxy to generate a network file.
2. Open the dataset and select **HIV-Trace Viewer** from the visualization menu.
3. Explore the interactive network in the browser.

## Requirements
- Galaxy 25.0 or newer
- Modern web browser with JavaScript enabled
npm package: @galaxyproject/locuszoom
Description: This is a starter template for building custom visualizations using [Galaxy Charts](https://github.com/galaxyproject/galaxy-charts), a modern framework for Galaxy visualization development based on [Vue 3](https://vuejs.org/) and [Vite](https://vitejs.dev
Latest version: 0.0.9

# <img src="https://cdn.jsdelivr.net/gh/galaxyproject/galaxy-charts/docs/public/galaxy-charts.svg" alt="Galaxy Charts Logo" width="24" /> Galaxy Charts Starter

This is a starter template for building custom visualizations using [Galaxy Charts](https://github.com/galaxyproject/galaxy-charts), a modern framework for Galaxy visualization development based on [Vue 3](https://vuejs.org/) and [Vite](https://vitejs.dev/).

Use this repo as a starting point for your own Galaxy visualization plugins.

---

## 🚀 Quick Start

1. **Create your visualization project** using this template:

    ```bash
    npx degit guerler/galaxy-charts-starter my-viz
    cd my-viz
    npm install
    npm run dev
    ```

2. **Open your browser** to [http://localhost:3000](http://localhost:3000) to start developing.

3. **Develop your plugin** inside the `src/plugins` directory.

---

## 📦 What's Included

- ⚡ Vite for fast dev server and hot module replacement
- 🧩 Galaxy Charts plugin system
- 🎨 Vue 3 setup with scoped components
- 🧪 Example plugin for reference
- 🛠️ Pre-configured for connecting to Galaxy datasets

---

## 📘 Learn More

- [Galaxy Charts Documentation](https://galaxyproject.github.io/galaxy-charts/)
- [Galaxy Charts Repository](https://github.com/galaxyproject/galaxy-charts)