Installation

Pip package

With Python 3.8 or higher, run:

pip install ms2pip

Compiled wheels are available for various Python versions on 64bit Linux, Windows, and macOS. This should install MS²PIP in a few seconds. For other platforms, MS²PIP can be built from source, although it can take a while to compile the large prediction models.

We recommend using a venv or conda virtual environment.

Conda package

Install with activated bioconda and conda-forge channels:

conda install -c defaults -c bioconda -c conda-forge ms2pip

Bioconda packages are only available for Linux and macOS.

Docker container

First check the latest version tag on biocontainers/ms2pip/tags. Then pull and run the container with:

docker container run -v <working-directory>:/data -w /data quay.io/biocontainers/ms2pip:<tag> ms2pip <ms2pip-arguments>

where <working-directory> is the absolute path to the directory with your MS²PIP input files, <tag> is the container version tag, and <ms2pip-arguments> are the ms2pip command line options (see Command line interface).

For development

Clone this repository and use pip to install an editable version:

pip install --editable .

Optionally, add the [dev,docs] extras to install the development and documentation dependencies:

pip install --editable .[dev,docs]