Installation

Python package

Install with pip Install with conda

MS²Rescore is installable as a Python package on Windows, macOS and Linux.

In a fresh virtual environment, run:

pip install ms2rescore

Or, in a fresh conda environment, run:

conda install -c bioconda ms2rescore

Bioconda packages are only available for Linux and macOS.

Windows installer

Get for Windows

Download the .exe file from the latest release and go through the installation steps. If Microsoft Defender SmartScreen displays a warning, click “More info” and then click “Run anyway”.

Docker container

Pull with Docker

First check the latest version tag on biocontainers/ms2rescore/tags. Then pull and run the container with:

docker container run -v <working-directory>:/data -w /data quay.io/biocontainers/ms2rescore:<tag> ms2rescore <ms2rescore-arguments>

where <working-directory> is the absolute path to the directory with your MS²Rescore input files, <tag> is the container version tag, and <ms2rescore-arguments> are the ms2rescore command line options (see Command line interface).

Installing Percolator

To use Percolator as rescoring engine, it must be installed separately. Percolator is available for most platforms and can be downloaded from the GitHub releases page. Ensure that the percolator executable is in your PATH. On Windows, this can be done by checking the Add percolator to the system PATH for current user option during installation:

Percolator installation on Windows

Note

Alternatively, Mokapot can be used as rescoring engine, which does not require a separate installation.

For development

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

pip install --editable .