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.

Optional dependencies

Some features require additional dependencies that are not installed by default. Install them with the relevant extra, for example:

pip install ms2rescore[mumble]

  • mumble: enables the Mumble PSM generator, which proposes candidate modifications for PSMs with an unresolved precursor mass shift. Mumble is beta software; see Open modification searching with Mumble before enabling it.

  • idxml: enables reading OpenMS idXML PSM files.

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).

For development

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

pip install --editable .