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 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.

1. 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.

2. Python >= 2.6 (including Python 3!)

   • This will come installed with OS X or any respectable *NIX distro.

3. 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
   

4. 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

5. 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

1. 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 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.