hisakatha / mirnylib-legacy

A legacy repository. Useful functionality was ported to cooltools.lib.numutils.

mirnylib

Notice 6/14/19

This repository is not actively maintained.

Please see cooler (https://github.com/mirnylab/cooler/), cooltools (https://github.com/mirnylab/cooltools), and distiller (https://github.com/mirnylab/distiller-nf) for actively maintained & developed Hi-C analysis tools.

Installation

Use pip. There is also an install script (Linux only).

Get the latest:

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

Or clone the repo, build extensions, and install in development mode:

$ hg clone https://bitbucket.org/mirnylab/mirnylib
$ cd mirnylib
$ python setup.py build_ext --inplace
$ pip install -e .

Installation Requirements

Python 2.7/3.3+

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.

Required:

• numpy (1.6+)
• scipy
• matplotlib
• h5py
• biopython
• joblib (0.6.3+)
• bx-python (preferably from the bitbucket repo by james_taylor)
• Cython (0.16+) to build Cython extensions from .pyx source (C files no longer provided)

Notes

We highly recommend using the conda package/environment manager if you have trouble building the core scientific Python packages.

$ conda install numpy scipy matplotlib h5py cython

See also

hiclib