.. _installation: Installation ------------ Supported systems ~~~~~~~~~~~~~~~~~ :Hardware: 1GB of RAM and a 64-bit operating system. RAM usage heavily depends on what you're doing, but 1GB is the bare minimum if you disable caching. :Software: Tested on OS X 10.8 and on Ubuntu 11.10, but should run fine on any other \*NIX flavour as long as the prerequisites are fulfilled. .. warning:: Windows is not supported - not even Cygwin! Pre-installation requirements ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In order to install :mod:`pyDNase`, the following software is required. Most people will already have most of these on their system. I have attempted to list them in the order that you need to install them in. #. A compiler suite You can check by opening up the terminal and typing :: $ clang --version or :: $ gcc --version As long as you get a response from one of these, you're good to go. Failing that... * **On OS X < 10.7.3:** Install "Xcode" from https://developer.apple.com/downloads/ * **On OS X >= 10.7.3:** Install "Command Line Tools for Xcode" from https://developer.apple.com/downloads/ (you can also install Xcode, but this is overkill) * **On Ubuntu:** Install with ``sudo apt-get install build-essentials`` .. note:: If you're using another \*NIX distro, I assume you know what you're doing. #. Python_ >= 2.6 (including Python 3!) * This will come installed with OS X or any respectable \*NIX distro. #. pip_: Used for automated installation of Python packages. If you don't already have pip_ installed, you can use the following command to install it :: $ curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py | python #. samtools_ * **On OS X** the simplest way to install samtools_ is using the homebrew_ command ``brew tap homebrew/science`` followed by ``brew install homebrew/science/samtools``. * **On Ubuntu** you can use ``sudo apt-get install samtools`` #. bedtools_ * **On OS X** the simplest way to install bedtools_ is using the homebrew_ command ``brew tap homebrew/science`` followed by ``brew install homebrew/science/bedtools``. * **On Ubuntu** you can use ``sudo apt-get install bedtools`` Optional installs ~~~~~~~~~~~~~~~~~ #. pybedtools_ * This is only required if you want to use the ``dnase_bias_estimator.py``. Provided you installed pip_, you should be able to simply run :: $ pip install pybedtools Installing :mod:`pyDNase` ~~~~~~~~~~~~~~~~~~~~~~~~~ To install, simply :: $ pip install pyDNase This will attempt to download, compile, and install the python dependencies (``clint``, ``numpy``, ``pysam``, and ``matplotlib``) automatically. However, due to a myriad of reasons it might not work. If this is the case, go and install these manually in said order, then try ``pip install pyDNase`` once more. .. _pybedtools: https://pythonhosted.org/pybedtools/ .. _python: http://www.python.org/ .. _samtools: http://www.htslib.org/ .. _bedtools: http://bedtools.readthedocs.org/en/latest/ .. _homebrew: http://brew.sh/ .. _NumPy: http://www.numpy.org/‎ .. _clint: https://github.com/kennethreitz/clint .. _pysam: https://code.google.com/p/pysam/ .. _SciPy: http://www.scipy.org/‎ .. _matplotlib: http://www.matplotlib.org .. _pip: https://pypi.python.org/pypi/pip