Getting started

HiFive requires Python 2.7. To check your version, run:

> python -V

Installing HiFive

HiFive can be obtained from HiFive using the following command:

> hg clone https://bitbucket.org/bxlab/hifive/

or alternatively, download a snapshot of the repository using the following commands:

> wget https://bitbucket.org/bxlab/hifive/downloads/hifive_v2.2.tar.bz2
> tar -xjf hifive_v2.2.tar.bz2

HiFive depends on a few packages and has several others that extend its functionality.

Required Packages

• Scipy
• Numpy
• h5py

Recommended Packages

• Sphinx for generating local documentation
• Pysam for reading BAM files
• Pyx for generating PDF images
• PIL for generating bitmap images
• mpi4py for utilizing MPI capabilities of several HiC functions
• mlpy for modeling 3D structure

For a more traditional Python installation simply setup a virtualevn for HiFive (this example creates one in .venv in your home directory) and then install the required packages and HiFive.

> virtualenv ~/.venv; source ~/.venv/bin/activate

To install HiFive, simply enter the directory that the repository was cloned or downloaded to and use the following command:

> python setup.py install

If you wish to install HiFive in a location other than the default, you can use the prefix option:

> python setup.py install --prefix=/your/desired/path

Installing Documentation

In order to build HiFive’s documentation locally, you need to execute the following command:

> cd doc
> make html

This will create the documentation suitable for viewing with a web browser. In order to create a pdf version of the documentation, simply run the following:

> cd doc
> make latexpdf