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 3.9+
• 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

Session state is stored in ~/.galaxy-cli/session.json. It is intended for a single active writer; for parallel automation or multiple concurrent agents, pass --history-id explicitly instead of relying on shared session state.

Usage

galaxy-cli history list
galaxy-cli history create "My Analysis"
galaxy-cli tool search "bowtie"
galaxy-cli workflow list
galaxy-cli workflow list | jq .

galaxy-cli emits human-readable text when stdout is a terminal and JSON when stdout is piped or redirected. Use --json to force JSON in a terminal, or --no-json to force text output.

Run the REPL:

galaxy-cli

Tests

python3 -m pytest galaxy_cli/tests/ -v