🌌 Galaxy App

Galaxy App is a Python library that simplifies interaction with a Galaxy server — a powerful platform for accessible, reproducible, and transparent computational biomedical research.

This library helps developers easily create applications or workflows that communicate with Galaxy instances through a Pythonic interface.

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Installation

You can install the galaxy-app package using pip:

pip install galaxy-app

Note: It is strongly recommended to install this package inside a virtual environment to avoid conflicts.

Create and activate a virtual environment (recommended):

# Create virtual environment
python3 -m venv venv

# Activate it (Linux/macOS)
source venv/bin/activate

# Activate it (Windows)
venv\Scripts\activate

Then install:

pip install galaxy-app

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Quick Start

Here’s a simple example to connect to a Galaxy instance and list available tools:

from galaxy.app import GalaxyApp

# Connect to your Galaxy instance
app = GalaxyApp("https://usegalaxy.org", api_key="YOUR_API_KEY")

# List all tools
tools = app.tools.list()
for tool in tools:
    print(tool["name"])

💡 Replace "YOUR_API_KEY" with your actual Galaxy API key. You can get this from your Galaxy user account (usually under "User > Preferences > API key").

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Or install from GitHub:

git clone https://github.com/iCog-Labs-Dev/galaxy-app.git
cd galaxy-app
pip install .

Then

python -m galaxy_app

Features

• Connect to any Galaxy instance using API key
• List available tools and workflows
• Submit jobs to Galaxy tools
• Retrieve job status and results
• Manage datasets, histories, and workflows

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Documentation

Currently, the package has limited documentation. You can start by exploring:

• Galaxy-app Vs Bioblend
• Galaxy API docs
• Source code (GitHub page if available)
• PyPI page

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Troubleshooting

• Authentication error: Make sure your API key is valid.
• Connection error: Ensure your Galaxy server URL is correct and accessible.
• Missing dependencies: Ensure you are using a compatible Python version (usually Python 3.6+).

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🤝 Contributing

As of now, contributions may not be open, but if any issue open, feel free to fork the project and explore the code.

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Need Help?

If you're new to Galaxy or bioinformatics pipelines in general, consider reading:

• Galaxy Training Network
• Galaxy Community Hub