There are three main components to Trident. Initial results are produced with a single executable written in C. Additionally, there are a set of post-processing tools available to analyze trident data. Finally, data may be presented using the web user interface presented here. All three are available under the GNU General Public License version 3. These components can be obtained individually (below). Trident was built and tested on CentOS 6. However, the trident executable has been used on Mac OSX 1.6 and Windows XP and 7, with the Windows version being built using Cygwin.
The Trident executable is available as source code. The current release may be downloaded here.
Also, the source code repository is available using git. A copy of the source code be obtained by cloning the repository, using the command:
git clone https://github.com/stjude/trident.git
Trident is written in C and is built using GNU Autotools. To build trident, in a terminal, change to the top Trident source directory. Then run
./configure && make
Depending on the score threshold, trident output can be very lengthy. To facilitate efficient and simple data extraction and analysis, the trident package comes with Hadoop Map Reduce programs. The latest trident score map reduce program is available as a jar file. Also, the hadoop code is located in the hadoop subdirectory of the main source code distribution. The java main class is TridentScoreMR. This program requires an input file name as a command line argument. For example, to count the number of Energy-Score pairs, run:
hadoop jar TridentScoreMR.jar TridentScoreMR /user/dcoss/hs/chr18/chr18.out
Multiple python script are available for preparing and analyzing data from trident. For a detailed description of the trident modules available, see the trident python api page. The python code is located in the python subdirectory of the main source code distribution. Also, for linux, the trident python package and scripts may be downloaded as a Python Egg built for Python 2.6 or Python 2.7.
The trident python code may be build from source using setuptools. To build and install the python code, in the python subdirectory, run:
python setup.py install
This website was developed to allow the user to search and visualize trident results. A template trident website is available as a django application. The source may downloaded as a source package or cloned from the git repository: by running:
git clone https://github.com/stjude/trident_web.git
The website requires Apache, Python 2.7 and Django 1.5. To setup Apache to run trident web, the apache configuration files must be changed to include the trident web path. An example apache configuration file is located in the apache subdirectory of the Trident Web directory.