| 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 |
| 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:
- Python >= 2.7
- Numpy >= 1.4.0
- Scipy >= 0.7.0
- Scikit-learn >= 0.14
- Pysam >= 0.7.5
- HTSeq >= 0.6.1
- hmmlearn >= 0.0.1
- mpmath
- ngslib
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.