fermo_gui

fermo_gui is the graphical user interface for the metabolomics data analysis pipeline fermo_core. It allows to start new analysis jobs, load existing session files, and visualize results.

For more information about FERMO, fermo_gui, or fermo_core, see the Documentation.

Nota bene: fermo_gui has only been tested on Linux systems. While the Docker-installation is likely to work on other systems as well, they are not officially supported. See Fermo Online for a user-friendly installation-free version.

Table of Contents

• Installation and Quickstart
• Usage
• Attribution
• For Developers
• Contributing

Installation and Quickstart

With docker from GitHub

• Install docker and docker-compose
• Download or clone the repository
• (Change into the fermo_gui base directory if not already present)
• Run docker-compose up --build. This will compose the docker container, install all dependencies and start the application.
• Open the application in any browser with the URL http://0.0.0.0:8001/
• To terminate the container, simply hit ctrl+c

Usage

For more information about FERMO, fermo_gui, or fermo_core, see the Documentation.

Attribution

License

FERMO is licensed under the MIT License.

Authors

• Mitja M. Zdouc [email protected]
• Hannah E. Augustijn [email protected]

Publications

See FERMO online for information on citing fermo_gui.

Versions

All previous version of FERMO can be accessed via its Zenodo repository.

For Developers

Dependencies

A list of dependencies can be found in the file pyproject.toml.

Installation and Setup

• Clone the repository to your local machine and enter the fermo_gui source directory
• Install python 3.11
• Install pip install pipx
• Install pipx install hatch
• Run hatch -v env create dev
• Run hatch run dev:pre-commit install
• Install redis-server with sudo apt-get install redis-server
• Run the application with hatch run dev:flask --app fermo_gui run --debug
• In a separate command line window, run hatch run dev:celery -A make_celery worker --loglevel ERROR

Config file

The flask application automatically reads configuration settings from a config.py file in the instance directory in the fermo_gui source directory (not in version control for security reasons). If not available, fermo_gui will employ default settings, assuming that the application runs offline. These default settings must not be used if the application is to be deployed to production. The following default settings are used:

SECRET_KEY: str
ONLINE: bool = True
MAX_RUN_TIME: int = 3600
CELERY: dict = {
    "broker_url": "redis://localhost",
    "result_backend": "redis://localhost",
    "task_ignore_result": True,
    "task_soft_time_limit": 3600
}
MAIL_USERNAME: str
MAIL_PASSWORD: str
MAIL_DEFAULT_SENDER: str
MAIL_SERVER: str
MAIL_PORT: int
MAIL_USE_TLS: bool
MAIL_USE_SSL: bool

Further, the number of workers can be adjusted in the entrypoint_docker.sh script.

Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. Please see Contributing for more information on getting involved. Contributors agree to adhere to the specified Code of Conduct. For technical details, see the For Developers pages in the Documentation.