The RGT-Viz will automatically install all python package requirements. However, we highly recommend that you pre-install scipy and it is desirable that numpy is also pre-installed. If you experience any problems with the installation regarding the package requirements, you can try to install these packages individually (please visit their website listed bellow for more information). The package requirements for the most current version is:
In the introduction, it was explained how to install the package in a fast way if you have superuser privileges. However, if you don’t have such privileges (for instance, you are running the tool in a server) you can install the package manually using the prefix scheme. This can be easily performed (for python version X.Y) by typing the following command:
export PATH=$PATH:~/app/bin export PYTHONPATH=$PYTHONPATH:~/app/lib/pythonX.Y/site-packages mkdir -p ~/app/bin ~/app/lib/pythonX.Y/site-packages python setup.py install --prefix=~/app --rgt-tool=viz
The above command will install the package to your ~/app folder. You can change the location of this folder to whichever you want. Note that in the above commands we made some modifications to your PYTHONPATH and PATH variables. The PYTHONPATH variable should contain all the paths to python libraries and the PATH variable should contain the paths to all binaries you want to execute.
Furthermore, we provide some extra options for RGT packages installation:
1. Data Path: RGT uses data such as the genome, genome size, default hidden Markov models, etc. All these data will be installed by default to ~/rgtdata. However you may want to modify such path by using this option.
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 RGT-Viz please use this as in the example below.
The example below shows an example of installation using all these options:
python setup.py install --prefix=~/app --rgt-data-path=~/app --rgt-tool=viz