The recommended way of installing RGT is via pip, the main python package manager. After installing pip, type:
pip install --user RGT
This will install the full RGT suite with all dependencies. However, we highly recommend that you pre-install the following dependencies:
pip install --user cython numpy scipy
If you do not want to use pip, or cannot, it’s very easy to install RGT manually. Either download here the latest RGT release or clone the github repository:
git clone https://github.com/CostaLab/reg-gen.git
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). The same caveat exists about dependencies: if you have troubles, manually install at least cython, numpy and scipy and then try again installing RGT.
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 the core library please use this:
python setup.py install --user --rgt-tool=core
Or if you wish to install more than one tool, you can do as follows:
python setup.py install --user --rgt-tool=THOR,motifanalysis