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This is the officially recommended command line tool for normal users and are encouraged to use this. It implements all the functionality in more than 100 command and subcommands. As per OpenCGA design, these commands are one-to-one mapping of Resources from REST web services  and subcommands are mapping to end-points. These commands underneath makes REST calls to carry out operations, thus any user who has access to REST cluster can execute these commands. 

For example, in the following URL, samples is the resource :

http://bioinfoint.hpc.cam.ac.uk/opencga-1.3.0-dev/webservices/rest/v1/samples/search

so the corresponding command in commandline is :

./opencga.sh samples

and search is the endpoint so corresponding subCommand is : 

./opencga.sh samples search