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You don't tell us what doesn't work, but assuming that you're getting complaints from catkin_make that it can't find certain ROS pkgs or that catkin_make itself can't be found: do you source /path/to/the/catkin_ws/devel/setup.bash (or equivalent for /opt/ros/$distro/setup.bash) before invoking catkin_make?

You don't tell us what doesn't work, but assuming that you're getting complaints from catkin_make that it can't find certain ROS pkgs or that catkin_make itself can't be found: do you source /path/to/the/catkin_ws/devel/setup.bash (or equivalent for /opt/ros/$distro/setup.bash) before invoking catkin_make?

You don't tell us what doesn't work, but assuming that you're getting complaints from catkin_make that it can't find certain ROS pkgs or that catkin_make itself can't be found: do you source /path/to/the/catkin_ws/devel/setup.bash (or equivalent for /opt/ros/$distro/setup.bash) before invoking catkin_make?

Edit:

I think catkin_make itself cannot be found. I have this in my ~/.bashrc:

source /opt/ros/kinetic/setup.bash
source /home/felix/sailing/bord-pc/devel/setup.bash
export BOARD_PC_WORKSPACE=/home/felix/sailing/bord-pc

And is your $HOME/.bashrc used by whatever/who-ever is running the git server? If not, your .bashrc will not have any influence.