Maldi-Tools

This repository contains scripts for extracting images from the TIMS TOF MALDI 2 with a user defined target library.

Installation Instructions

Conda

The fastest way to get up and running with Maldi Tools is to create a conda environment. You will need any flavor of conda. Some options include:

• Miniforge (Recommended as it contains conda-forge)
• Anaconda (also works)
• Miniconda (also works)

Install Maldi-Tools

Once you have any one of these installed, clone the repository with:

git clone maldi-tools

Then change the directory to maldi-tools and create the environment:

conda env create -f environment.yml

This will install all the dependencies and the most up-to-date version of maldi-tools.

Using Maldi-Tools

Maldi-Tools can be started by first activating the Conda environment with:

conda activate maldi-pipeline

and then the Jupyter interface can be started with:

jupyter lab

Development

Maldi-Tools is a poetry project and development requires python-poetry and pre-commit.

We recommend installing both with pipx.

For development, after cloning the repository, create the development environment and install dependencies for maldi-tools, development dependencies and testing dependencies with:

poetry install --with dev,test

Next, install the repo's pre-commit hooks with:

pre-commit install --install-hooks

Pre-commit hooks will sort imports, fix formatting, and lint your code for you. They run on each commit, but you may also run them manually with:

pre-commit run --all-files

Tests can be run with:

poetry run pytest

Issues?

Maldi-Tools is in early, active development. Please submit an issue for any bugs, or ideas for feature requests.