BINOCh
Binding Inference from Nucleosome Occupancy Changes

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The latest version of BINOCh is BINOCh.1.0.0.

Requirements

1. Python version 2.5.1 or later.
2. Python package Numpy, version 1.3 or later.
   

Installation Steps

Installation instructions for Unix-like operating systems (UNIX, Linux, or Mac OS X):

1. Download DNA sequence data for your genomes from UCSC and unzip, for example sequence for human genome version
   hg18
2. If you wish to filter sequence using a evolutionary conservation criterion download PhastCons data from UCSC and unzip. Downloading PhastCons data is optional and BINOCh will work without this data. For example if you intend to filter human genome hg18 sequence conservation relative to 17 species you will need to download these hg18 PhastCons files.
3. Extract BINOCh-x.x.x.tar.gz by typing on the command line:
   tar -xvf BINOCh-x.x.x.tar.gz
4. Change directory to the directory:
   cd BINOCh-x.x.x/src/cistrome/data/
   Copy the file datapath.conf.sample to datapath.conf:
   cp datapath.conf.sample datapath.conf
   then edit the paths in src/cistrome/data/datapath.conf to point to the genome sequence and PhastCons files. DO NOT edit the src/cistrome/data/datapath.conf.sample file.
5. Go back to the base BINOCh directory (i.e. ./BINOCh-x.x.x) and run the installation script:
   cd ../../../
   python setup.py build
   python setup.py install
   Note that the installer must have the proper security privileges to install BINOCh at /usr/local/bin. If you wish to install this package locally in the base directory $HOME/local do this:
   python setup.py install --prefix $HOME/local
   Then, add a line to the log-in shell script (i.e. .bashrc in case of bash shell) to specify the path to your python packages. This line should look similar to this:
   export PYTHONPATH=$PYTHONPATH:$HOME/lib/python2.5/site-packages
   but will depend on which version of Python is installed on your machine and the directory in which it is installed.

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