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 Python2.7 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
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.
Or, if you have multiple RGT installations? Let’s remove all of them in your computer by the instruction at the end of this page.
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:
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
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
Remove multiple installation
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.