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Installation
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Python package
==============

.. image:: https://flat.badgen.net/badge/install%20with/pip/green?icon=pypi
    :alt: Install with pip
    :target: https://pypi.org/project/ms2rescore/

.. image:: https://flat.badgen.net/badge/install%20with/conda/green?icon=conda
    :alt: Install with conda
    :target: https://anaconda.org/bioconda/ms2rescore

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

In a fresh `virtual environment <https://docs.python.org/3/library/venv.html>`_, run::

    pip install ms2rescore


Or, in a fresh `conda environment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_, run::

    conda install -c bioconda ms2rescore

Bioconda packages are only available for Linux and macOS.


Windows installer
=================

.. image:: https://flat.badgen.net/badge/install%20for/windows/blue?icon=windows
    :alt: Get for Windows
    :target: https://github.com/compomics/ms2rescore/releases/latest

Download the ``.exe`` file from the
`latest release <https://github.com/compomics/ms2rescore/releases/latest>`_
and go through the installation steps. If Microsoft Defender SmartScreen displays a warning, click
"More info" and then click "Run anyway".


Docker container
================

.. image:: https://flat.badgen.net/badge/pull/biocontainer/blue?icon=docker
    :alt: Pull with Docker
    :target: https://quay.io/repository/biocontainers/ms2rescore

First check the latest version tag on
`biocontainers/ms2rescore/tags <https://quay.io/repository/biocontainers/ms2rescore?tab=tags>`_.
Then pull and run the container with:

.. code-block:: bash

   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 :ref:`Command line interface`).


Installing Percolator
=====================

To use :ref:`percolator` as rescoring engine, it must be installed separately. Percolator is
available for most platforms and can be downloaded from the
`GitHub releases page <https://github.com/percolator/percolator/releases/latest>`_. 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:

.. figure:: ../_static/img/percolator-install-path.png
   :width: 60%
   :alt: Percolator installation on Windows

.. note::
   Alternatively, :ref:`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:

.. code-block:: bash

   pip install --editable .