HowToCompile.txt

Compiling the source code

Requirement: GNU gcc8.2 or higher. Please change the name (CXX) of the compiler 
	in the Makefile. 

If on MacOS, please uncomment the compiler flags (CXXFLAGS) in the Makefile. (Marked #MacOS). 

On MacOS you may need to run:
	> brew install libomp

To locate the source directory:
	> cd src	

The following command makes the required directories: 
	> make bin

The following command makes the binary that is located under the ``bin'' directory:
	> make tr -j

To find the binary:
	> cd ../bin

To find help information:
	> LtrDetector -help

Example run with the defaults:
	> LtrDetector -chromDir ~/Data/zmays/Fa -destDir ~/Data/zmays/detector

Example run on 4 cores
	> LtrDetector -chromDir ~/Data/thaliana/Fa -destDir ~/Data/thaliana/detector -nThreads 4


To run visualization tool:
	Step 1: Run LtrDetector with these three flags -rawScores -cleanedScores -bedFormat 
	> LtrDetector -chromDir ~/Data/thaliana/Fa -destDir ~/Data/thaliana/detector -rawScores -cleanedScores -bedFormat

	Step 2: To run the visualization tool on chr1, pass LTR-RTs found in chr1 (.bed), output directory where the graphs will be stored, and the scores file (raw or cleaned).
	> python visualize.py ~/Data/thaliana/detector/chr1Detector.bed ~/Data/thaliana/detector/test ~/Data/thaliana/detector/chr1RawScores.csv