Overview

mirnylib

Installation

The easiest way is to use pip, but see notes below:

$ pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz

Installation Requirements

Python 2.6 or 2.7

It is probably a good idea to upgrade to the latest version of setuptools and pip. Follow the PyPA's guide.

Python dependencies

Required:

Getting the basic Scientific Python stack (numpy/scipy/matplotlib) can be trickier on some platforms than others. For more details, see the instructions on scipy.org. You should already have these dependencies installed and running correctly before attempting to install this package.

  • numpy (1.6+)
  • scipy
  • matplotlib

The following dependencies are automatically installed by setuptools if missing:

  • biopython
  • joblib (0.6.3+)
  • bx-python (preferably from the bitbucket repo by james_taylor)
  • h5py (see note below)

Non-Python dependencies

  • For the h5py package to install properly, you need to have the shared library and development headers for HDF5 1.8.4 or newer installed (libhdf5-dev or similar). See the h5py docs for more information.

Build dependencies

  • Cython (0.16+) to build Cython extensions from .pyx source (recommended but optional; C files are provided)

  • A C compiler to compile the C extensions