CLI harness for the Galaxy bioinformatics platform
Project description
cli-anything-galaxy
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.
Prerequisites
- Python 3.10+
- A running Galaxy server
- A Galaxy API key from your target instance
Installation
python3 -m pip install -e .
Verify installation:
cli-anything-galaxy --version
Configuration
Set your Galaxy server URL and API key:
export GALAXY_URL=https://usegalaxy.org
export GALAXY_API_KEY=your-api-key
cli-anything-galaxy config test
Usage
cli-anything-galaxy history list
cli-anything-galaxy history create "My Analysis"
cli-anything-galaxy tool search "bowtie"
cli-anything-galaxy --json workflow list
Run the REPL:
cli-anything-galaxy
Tests
python3 -m pytest cli_anything/galaxy/tests/ -v
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