Download & Installation

Version Comments
ODIN-0.4.1 GPL v3 licence, bigfixes
ODIN-0.4 improvement of read extension size estimation
ODIN-0.3.2 support of Mac OS, small bugfix, when input-DNA does not overlap with IP-DNA
ODIN-0.3.1 use HMM of package hmmlearn instead of sklearn
ODIN-0.3 p-value correction, bugfixes, output directory
ODIN-0.2 bugfixes, additional narrowPeak output
ODIN-0.1.1 fix chrom size bug, BigWig construction. Since peaks are not merged, please do not use this version!
ODIN-0.1alpha paper version

Feel free to post your question in our googleGroup or write an e-mail: rgtusers@googlegroups.com

Installation Requirements

ODIN’s installation setup will automatically install all python package requirements. However, we highly recommend that you pre-install scipy and numpy. The python package requirements are:

Important: ODIN uses wigToBigWig from the UCSC utilities website to handle BigWig files. ODIN therefore automatically copies this tool in your bin directory. The wigToBigWig version ODIN copies is for a 64bit linux system. If you have another system (32bit, macsOS), please copy the appropriate binaries by yourself and make sure that they are contained in your $PATH variable. You can load the BigWig files in IGV to visualize the experiment.
ODIN is tested with Python 2.7.6, Numpy 1.8.1, Scipy 0.13.3, Scikit-lean 0.15.2, Pysam 0.7.5, mpmath 0.18 and hmmlearn 0.1.1 on a 64bit Linux (Ubuntu) machine.

Customized Installation

If you do not have superuser rights on your system, you can install ODIN by:

python setup.py install --prefix=<INSTALLATION-FOLDER> --rgt-tool=ODIN

Make sure that your PATH variable contains <INSTALLATION-FOLDER>.

A folder rgtdata, containing annotation files such as chromosome sizes, will be created in your homefolder. You can change the path with

--rgt-data-path

Please see here for more information about the rgtdata folder.