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I tested the following yaml file

myCustomPkg:
    ubuntu:
        pip:
            packages: ["git+https://github.com/user/repo.git@master"]

And it seemed to work. The simulate install gave the following command:

> rosdep check myRosPkg --os=ubuntu:xenial -i
rosdep detected OS: [elementary] aliasing it to: [ubuntu]
System dependencies have not been satisified:
  sudo -H pip install -U git+https://github.com/user/repo@master

By taking into account @tfoote comment, I tested the following yaml file

myCustomPkg:
    ubuntu:
        pip:
            packages: ["git+https://github.com/user/repo.git@master"]

And it seemed to work. The simulate install gave the following command:

> rosdep check myRosPkg --os=ubuntu:xenial -i
rosdep detected OS: [elementary] aliasing it to: [ubuntu]
System dependencies have not been satisified:
  sudo -H pip install -U git+https://github.com/user/repo@master