galaxy-cli 1.0.0

CLI harness for the Galaxy bioinformatics platform

galaxy-cli

CLI harness for the Galaxy bioinformatics platform. It wraps Galaxy's REST API to provide command-line and REPL access to histories, datasets, tools, workflows, jobs, and libraries.

This project was initially generated with cli-anything and then refined into the standalone galaxy-cli package.

Prerequisites

• Python 3.10+
• A running Galaxy server
• A Galaxy API key from your target instance

Installation

Install from PyPI with uv or pip:

uv tool install galaxy-cli

python3 -m pip install galaxy-cli

For local development from this repository:

python3 -m pip install .

Verify installation:

which galaxy-cli
galaxy-cli --version

Configuration

Set your Galaxy server URL and API key:

export GALAXY_URL=https://usegalaxy.org
export GALAXY_API_KEY=your-api-key

galaxy-cli config test

Usage

galaxy-cli history list
galaxy-cli history create "My Analysis"
galaxy-cli tool search "bowtie"
galaxy-cli --json workflow list

Run the REPL:

galaxy-cli

Tests

python3 -m pytest cli_anything/galaxy/tests/ -v