Please take a look at the documentation in the doc subdirectory. They will contain the input file format and more explanations for running CCA.
To build the image where you downloaded the source, do
docker build -t cca .
in the directory with the Dockerfile. This is optional and one can instead pull the Docker image from the Docker hub by doing
docker pull tohsumirepare/cca
To run the program, please read the documentation in the docs directory. Then, once example files EX1.txt and EX1.repmap are ready in directory, for example, /Users/login/temp, then do
docker run --rm -it -v "/Users/login/temp:/home:rw" tohsumirepare/cca crisprCountsAnalysis COUNTS=EX1.txt REPMAP=EX1.repmap OUT_MAX=EX1
in the directory with the EX1.* files if you have pulled the Docker image. If you have compiled the code instead then do
docker run --rm -it -v "/Users/login/temp:/home:rw" cca crisprCountsAnalysis COUNTS=EX1.txt REPMAP=EX1.repmap OUT_MAX=EX1