Requirements and Installation¶
Requirements¶
Software¶
- Python 2.7.12+
- R >=3.1.2
- bedtools
- perl
- HiCUP
- bwa
- samtools>1.3
Python Modules¶
- mg-tool-api
- pylint
- pytest
- rtree
- pyenv and pyenv-virtualenv
- rpy2
- matplotlib
- pandas
- rtree
- numpy
- scipy
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”)