Download & Installation

 

Download

Although you can download the developer version via github, we also provide RGT stable releases. Please find the latest stable distributions of RGT in the following table:

Version Download Link Comments
0.9.5 Download
0.9.4 Download
0.9.3 Download Many improvements to all tools, both in functionality and performance.
0.0.1 Download First stable release of RGT.

 

Basic Installation

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.

Alternatively, you can clone the github repository:

git clone https://github.com/CostaLab/reg-gen.git

or download a specific release, then proceed to manual installation:

cd reg-gen
python setup.py install --user

Manual Dependency Installation

The RGT will automatically install all python package requirements. However, if you experience problems during manual installation you can try pre-installing a few critical libraries:

pip install --user cython numpy scipy

Advanced: Customized Installation

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-X.X.X
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 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