pyopenms 2.2.0

Table of Contents

• Introduction
• Installation
  • Binary installation
  • Source installation
• Testing
• License
• Documentation

Introduction

This package contains Python bindings for a large part of the OpenMS library (http://www.open-ms.de) for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).

The pyOpenMS package runs - like OpenMS - on Windows, Linux and OSX.

Installation

We provide binary packages for Python 2.6 and 2.7 on Windows (64 bit) and Linux 64 bit which makes the installation very straightforward with pip. For other platforms, please refer to the compilation instructions.

Binary installation

The current binaries require numpy 1.7.x. As we distribute the package as binary eggs, you have to use easy_install, installing with pip does not work:

$ easy_install pyopenms

Source installation

Download the latest OpenMS source from SVN (following the OpenMS documentation), configure and build.

Install Qt and then start with the dependencies of OpenMS itself:

$ git clone https://github.com/OpenMS/contrib.git
$ cmake .

Now you have to install the dependencies of pyOpenMS:

• Install Python (2.6 or 2.7)

• Install numpy (On OSX, numpy should already be installed. On GNU/Linux there should be packages for numpy (e.g. python-numpy for Ubuntu/Debian). On Windows, you can install it from Christoph Gohlkes webpage).

• Install setuptools, see the setuptools PyPI page .

• Use setuptools to install pip, autowrap and nose:

  $ easy_install pip
  $ pip install autowrap
  $ pip install nose
  

• Configure and build pyOpenMS:

  $ git clone https://github.com/OpenMS/OpenMS.git
  $ cmake -DPYOPENMS=ON .
  $ make pyopenms
  

This should build a file like pyopenms-1.10.1-py2.7-linux-x86_64.egg the folder ./pyOpenMS/dist of your build directory which you can distribute or install it from there:

$ cd pyOpenMS/dist
$ easy_install pyopenms-1.10.1-py-2.7-linux-x86_64.egg

Testing

pyOpenMS provides unittests, they are found under ./pyOpenMS/tests/ and can be executed using nosetests:

$ python run_nose.py

License

pyOpenMS is published under the 3-clause BSD licence, see ./pyOpenMS/License.txt

Documentation

pyOpenMS follows the OpenMS documentation very closely. Additionally, there is also a pyOpenMS Manual available. The online manual contains a complete record of every wrapped class and function while the documentation of the corresponding class or function can be inferred from the OpenMS online documentation.