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I'm not sure if I got your problem, but, you can init a catkin workspace using this:

First, create a folder where it'll be your workspace folder and your source folder:

$ mkdir -p my_workspace/src

After that, go to my_workspace folder and run it:

$ catkin_make

And done. Now it is just going to src folder and run it:

$ catkin_create_pkg pkg_name roscpp rospy etc