Sources
=======

Overview
--------

The source code of OpenMS, PyProphet and msproteomicstools is provided on
GitHub under the 3-clause BSD license. Please refer to the individual
repositories for information regarding obtaining, compiling and installing the
components.

OpenMS
------
OpenSWATH is fully integrated within `OpenMS <http://www.openms.org>`_. Please
obtain the latest version of OpenMS from `GitHub
<https://www.github.com/OpenMS/OpenMS>`_.

Instructions for compilation and installation can be obtained from the `OpenMS
documentation
<http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html>`_.

EasyPQP
---------
Please obtain the latest version of EasyPQP from `GitHub
<https://github.com/grosenberger/easypqp>`_.

The instructions for the installation of the EasyPQP :doc:`binaries` is
applicable here as well.

PyProphet
---------
Please obtain the latest version of PyProphet from `GitHub
<https://www.github.com/PyProphet/pyprophet>`_.

The instructions for the installation of the PyProphet :doc:`binaries` is
applicable here as well.

msproteomicstools & TRIC
------------------------
Please obtain the latest version of msproteomicstools from `GitHub
<https://github.com/msproteomicstools/msproteomicstools>`_.

The instructions for the installation of the msproteomicstools :doc:`binaries`
is applicable here as well.


DIAlignR
--------

Please obtain the latest version of DIAlignR from `GitHub <https://github.com/shubham1637/DIAlignR>`_.

The instructions for the installation of the DIAlignR :doc:`binaries` is applicable here as well.

ARYCAL
------

Please obtain the latest verson of ARYCAL from `Github <https://github.com/singjc/arycal>`_.

The instructions for building ARYCAL from source can be found on the `Github README Build from Source <https://github.com/singjc/arycal?tab=readme-ov-file#build-from-source>`_ section.

MOBI-DIK & diapysef
-------------------
Please obtain the latest version of diapysef from `GitHub
<https://github.com/Roestlab/dia-pasef/src/diapysef>`_.

The instructions for compilation and installation of diapysef :doc:`binaries`
is applicable here as well.