Download & Installation

These instructions are only to be attempted if you know what you are doing and the basic instructions failed. Please contact us on our Support group if you experience any problems.

Linux Installation

The recommended way of installing RGT is via pip, the main python package manager. After installing pip, type in this order:

pip install --user cython numpy scipy
pip install --user RGT

This will install the full RGT suite with all python dependencies. A few more libraries will be needed, but should be installed via your own distribution’s package manager.

MacOS X installation

Before installing via pip, we need to setup the environment. First of all, you need the basic command line utilities for compilation:

xcode-select --install

See this guide for more visual details. After this, you must install the Homebrew version of Python:

brew install python@2 boost llvm

Then the PATH needs to be updated:

# in the current terminal
export PATH="$(brew --prefix)/opt/python@2/libexec/bin:/usr/local/bin:$PATH"
# we make sure it persists
echo 'export PATH="$(brew --prefix)/opt/python@2/libexec/bin:/usr/local/bin:$PATH"' >> ~/.bash_profile
Finally, we can use pip but without –user:
pip2 install cython numpy scipy
pip2 install RGT

Setup Data folder

The RGT Data Folder must be configured after installing RGT, or some of the tools will not work. Follow this link to learn how.

By default, the folder named rgtdata is placed in your home directory after installation. If you need to put it in an alternative location (for example to use a single data folder for multiple users), you must put the full path to the RGTDATA environment variable. On Linux, you would need to copy the following line to your .bashrc file:

RGTDATA=/path/to/rgtdata

Advanced Installation

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, you can also decide to only install one or more tools, instead of the full suite, like so:

# installs the tools THOR and Motif Analysis
python setup.py install --user --rgt-tool=THOR,motifanalysis