Requirements and Installation

Requirements

Software

  • Python 2.7.12+
  • R >=3.1.2
  • bedtools
  • perl
  • HiCUP
  • bwa
  • GEM
  • TADbit
  • samtools>1.3

Python Modules

  • mg-tool-api
  • pylint
  • pytest
  • pandas
  • rtree

R Modules

  • argparser
  • devtools
  • Chicago

To Run runChicago.py and process_runChicago.py, the R script runChicago.R from https://bitbucket.org/chicagoTeam/chicago/src/ceffddda8ea392a1e84e4db9593f8fc35ac88048/chicagoTools/?at=master should be downloded and added to PATH.

Installation

Directly from GitHub:

1
git clone https://github.com/pabloacera/C-HiC.git

Using pip:

1
pip install git+https://github.com/pabloacera/C-HiC.git

Install R modules, use the following R code:

install.packages(“argparser”) install.packages(“devtools”) library(devtools) install_bitbucket(“chicagoTeam/Chicago”, subdir=”Chicago”)