RGT Motif Analysis uses the package MOODS to perform high-speed motif matching. Such package cannot be automatically installed by our setup procedure and should be manually installed by the user. You can either install it with pip:
pip install --user https://github.com/fabioticconi/MOODS/tarball/pypi-ready
Or download it here and type:
cd MOODS-python-1.9.3 python setup.py --user install
For more information please check MOODS website.
Besides MOODS, the Motif Analysis Tool will automatically install all python package requirements. However, we highly recommend that you pre-install the following dependencies:
pip install --user cython numpy scipy
because if missing, they often cause dependency resolution to fail.
If you experience any problems with the installation regarding the package requirements, you can try to install these packages manually (please visit their website listed bellow for more information). The package requirements for the most current version is:
If you do not want to use pip, or cannot, it’s very easy to install RGT manually. Download here the latest RGT release and then type:
cd reg-gen python setup.py install --user
This will install the full RGT suite in your HOME directory (it doesn’t require administrator privileges). In addition, the above command can be further refined as follows:
1. Data Path: RGT uses data such as the genome, genome size, position frequency matrices, etc. All these data will be installed by default to ~/rgtdata. However you may want to modify such path by using this option:
python setup.py install --user --rgt-data-path=~/app
WARNING: Some data types (such as the genome) are too big to be in our installation structure. Please download our full data package here and merge it with your installed rgtdata path.
Learn more about the RGT Data Folder.
2. RGT Tool: If this option is not used, all RGT tools will be installed. In order to install only Motif Analysis Tools please use this:
python setup.py install --user --rgt-tool=motifanalysis