fermo-core 0.6.0

Data processing/analysis functionality of metabolomics dashboard FERMO

fermo_core

fermo_core is a tool to process, analyze, and prioritize compounds from metabolomics data.

While primarily intended to be the backend processing module of the FERMO application, fermo_core can be used as a command line interface (CLI) for large-scale data processing and analysis or as library.

This README specifies the use of fermo_core as CLI. For a more user-friendly version of FERMO, see FERMO Online.

For more information, see the FERMO Metabolomics GitHub Organization page.

Table of Contents

• Installation
• Quick Start
• Usage
• Attribution

Installation

With pip from PyPI

• Install python 3.11.x
• Create a virtual environment (e.g. venv, conda) and activate it
• Run pip install fermo_core
• Once installed, run as specified in Run with pip

With hatch from GitHub

• Install python 3.11.x
• Install hatch (e.g. with pipx install hatch)
• Download or clone the repository
• (Change into the fermo_core base directory if not already present)
• Run hatch -v env create
• Once installed, run as specified in Run with hatch

With conda from GitHub

• Install conda (e.g. miniconda)
• Create a conda environment with conda create --name fermo_core python=3.11
• Activate the conda environment with conda activate fermo_core
• Download or clone the repository
• (Change into the fermo_core base directory if not already present)
• Run pip install -e .
• Once installed, run as specified in Run with conda

Quick Start

Run with pip

• fermo_core --parameters <your_parameter_file.json>

Run with hatch:

• hatch run fermo_core --parameters <your_parameter_file.json>

Run with conda:

• python3 fermo_core/main.py --parameters <your_parameter_file.json>

Usage

fermo_core can be used both as a command line interface as well as a library.

All parameters and input data are specified in a parameters.json file. This file must be formatted according to the JSON Schema specified in fermo_core/config/schema.json. See the example in example_data/case_study_parameters.json.

For more information on input and output files, their format, and their purpose, consult the Documentation.

Attribution

License

fermo_core is an open source tool licensed under the MIT license (see LICENSE).

Publications

See FERMO online for information on citing fermo_core.