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Yes, the command you posted is the right thing to do in this case. It allows rosdep to figure out what packages are either not installed from apt-get nor in the current workspace and then try to install those from apt-get.

$ rosdep install --from-paths src --ignore-src --rosdistro indigo

The --from-paths src option tells rosdep to resolve dependencies for packages found in that folder, src, and the --ignore-src option tells rosdep not to try and install packages it finds in the folders given to --from-paths, in this case src. Without this option you get something like the error you got above which resulted because rosdep saw that scipio_simulation was a dependency of some other package so it would try to resolve it (check that it is installed else install it), but since it is not released rosdep cannot handle it and bails out.

One note is that you should do this:

$ mkdir -p /path/to/workspace/src
$ cd /path/to/workspace/src
$ git clone [url]

Rather than cloning the repo directly as src, as you suggested:

creates a catkin workspace, and does "git clone [repo url] src"