<commit_before>Binaries
========

Overview
--------

Precompiled or prepackaged versions of OpenMS, PyProphet and msproteomicstools are readily available for most supported platforms. 

.. warning::

   Please note that the published versions are always based on the latest `release` versions, however some functionality described online might only be available in the latest `development` builds.

OpenMS
------
OpenSWATH is completely integrated into `OpenMS <http://www.openms.org>`_. The current releases can be obtained from `GitHub <https://github.com/OpenMS/OpenMS/releases>`_. To make use of the latest developments, consider using the `nightly builds for Windows and macOS <https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/>`_.

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>`_.

PyProphet
---------

PyProphet requires Python 2.7 or Python 3. Windows users should install Anaconda. Mac and Linux users should be able to install PyProphet directly from GitHub. It is strongly recommended to install PyProphet within a `virtualenv <https://virtualenv.pypa.io/en/stable/userguide/>`_.

.. code-block:: bash

   # Install dependencies
   pip install numpy scipy scikit-learn pandas numexpr statsmodels Click matplotlib seaborn

   # Install PyProphet development version
   pip install git+https://github.com/PyProphet/pyprophet.git@master<commit_msg>Update binaries.rst<commit_after>Binaries
========

Overview
--------

Precompiled or prepackaged versions of OpenMS, PyProphet and msproteomicstools are readily available for most supported platforms. 

OpenMS
------
OpenSWATH is completely integrated into `OpenMS <http://www.openms.org>`_. The current releases can be obtained from `GitHub <https://github.com/OpenMS/OpenMS/releases>`_. To make use of the latest developments, consider using the `nightly builds for Windows and macOS <https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/>`_.

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>`_.

PyProphet
---------

PyProphet requires Python 2.7 or Python 3. Windows users should install Anaconda. Mac and Linux users should be able to install PyProphet directly from GitHub. It is strongly recommended to install PyProphet within a `virtualenv <https://virtualenv.pypa.io/en/stable/userguide/>`_.

.. code-block:: bash

   # Install dependencies
   pip install numpy scipy scikit-learn pandas numexpr statsmodels Click matplotlib seaborn
   
   # Install PyProphet release version
   pip install pyprophet

   # Alternative: Install PyProphet development version
   pip install git+https://github.com/PyProphet/pyprophet.git@master
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{'dir': 'git-commits-cleaned', 'id': '2309629', 'n_tokens_mistral': 814, 'n_tokens_neox': 776, 'n_words': 285}