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. Please notice that RGT only supports Python 3 now.
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 --no-binary 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.
Fail in installation?
Please try the following code if you didn’t install these libraries yet:
sudo apt-get install libcurl4-gnutls-dev zlib1g-dev
Then repeat the installation of RGT again.
Some errors are also due to older pip versions, so make sure to keep that updated:
pip install --user pip -U
Or, if you have multiple RGT installations, try removing all of them, then repeat the installation.
Before installing via pip, we need to setup the environment. First of all, you need the basic command line utilities for compilation:
See this guide for more visual details. After this, you must install the Homebrew version of Python:
brew install python boost llvm
Finally, we can use pip to install RGT. We suggest you do not use the –user
option, otherwise you’ll have to add another directory to your PATH.
pip2 install cython numpy scipy pip2 install RGT --no-binary RGT
Sorry. We don’t support windows environment this moment.
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:
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=motifanalysis,TDF
If you have multiple installation of RGT accidentally, please repeat the following command until no more RGT installation is detected.
pip uninstall RGT
Then please follow the instruction above for installation again.