PGFinder

A web-site for processing samples is available at PGFinder. For descriptions of the features of each version please refer to the Releases page or the Changelog. If you wish to use the development version please refer to the Installation and Usage documentation.

For an introduction to Peptidoglycan analysis please refer to the documentation.

Usage

PGFinder is available in two forms: a web-based User Interface (WebUI) at mesnage-org.github.io/pgfinder/ or a command line interface (CLI) Python package.

The command-line programme (find_pg) uses a YAML configuration file as input.

find_pg -c config.yaml

For details of using the CLI version including the configuration file please refer to the Usage section of the Documentation.

Installation

pgfinder

Detailed installation instructions can be found in the Installation section of the Documentation.

PGFinder is available from PyPI so can be installed with pip.

pip install pgfinder

It can also be installed directly from this repository

pip install "git+https://github.com/Mesnage-Org/pgfinder.git#egg=pgfinder&subdirectory=lib"

Or you can clone the repository and install it.

git clone https://github.com/Mesnage-Org/pgfinder.git
cd pgfinder/lib
pip install -e .

WebUI

A WebUI implemented using the Svelte framework is available. Detailed information of development is not currently provided but if you wish to run the WebUI locally you can do so. You will need the npm JavaScript package manager installed and you can then start the WebUI locally using the following and open the URL in your browser.

cd web
npm install
npm install vite            # Install the vite framework for building the site
npm run dev

Contributing

Contributions are welcome! Please refer to the detailed Contributing section of the Documentation which details how to setup and install all components, and setup/configure the development tools such as pre-commit.

Copying

This software is licensed as specified by the GPL License and LGPL License. Please refer to the COPYING and COPYING.LESSER files for further details.

Links

• Mesnage Lab
• PGFinder Online

References

• PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans | eLife