|THOR-0.1||new dependencies, GPL v3 license, bugfixes|
Feel free to post your question in our googleGroup or write an e-mail: firstname.lastname@example.org
THOR’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 >= 1.10.4
- Scipy >= 0.17.0
- Scikit-learn >= 0.17.1
- Pysam >= 0.9.0
- HTSeq >= 0.6.1
- hmmlearn < 0.2.0 (that is, version 0.1.1)
Important: THOR uses wigToBigWig, bedGraphToBigWig and bigWigMerge from the UCSC utilities website to handle BigWig files. THOR therefore automatically copies these tools in your bin directory. The tools THOR copies are 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.
THOR is tested with Python 2.7.6 on a 64bit Linux (Ubuntu) machine.
If you do not have superuser rights on your system, you can install THOR by:
python setup.py install --prefix=<INSTALLATION-FOLDER> --rgt-tool=THOR
Make sure that your PATH variable contains <INSTALLATION-FOLDER>.
If you want to install both, THOR and ODIN, by using the option:
A folder rgtdata will be created in your homefolder. You can change the path with
The rgtdata folder is not used by THOR. Please see here for more information.