There are three steps to make TDF ready to use:
- installation of TDF
- installation of Triplexator
- downloading of genome sequences and downloading of annotation files
1. Download & Install TDF
Please find the latest distributions of TDF in the following table:
|0.1.1||Download||First TDF stable version.|
The Triplex Domain Finder will automatically install all python package requirements. However, we highly recommend that you pre-install scipy and numpy. If you experience any problems with the installation regarding the package requirements, you can try to install these packages manually (please visit their website listed below for more information). The package requirements for the most current version are:
APT-GET installation on Ubuntu
If you have sudo permissions, one simple solution is to use apt-get to install python numerical packages scipy, numpy and matplotlib with the command:
sudo apt-get install python-matplotlib python-scipy
Then, extract the compressed file of TDF, go to the TDF folder and use the following command to install the tool:
sudo python setup.py install --rgt-tool=TDF
In the introduction it was explained how to install the package in a fast way if you have SUDO 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=TDF
The command will install the package to your ~/app folder. You can change the location of this folder to wherever you want. Note that in the above commands we made some modifications to the 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 package installation:
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.
WARNING: Some data types (such as the genome) are too big to be in our installation structure. Please check RGT Genome Configuration for further information for these big files.
2. Installation and Setting of Triplexator
After installation of Triplexator, put the path of Triplexator into $PATH.
3. Download the genome data for different organisms
For calculating the triplex forming sites, TDF requires the genome sequence in FASTA format. Besides, some features of TDF also requires annotation file for each genome. Before you run TDF on any organism, please make sure you download the genome data (see RGT Genome Configuration).