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The problem is that the .desktop doesn’t run the .bashrc sources, so your application doesn't know what ROS is along with all of its function (rosrun, roslaunch, etc.)

One way getting around it is adding to the exec command the source of ROS.

[Desktop Entry]
Version=1.0
Type=Application
Terminal=true
TerminalOptions=bash
Exec=bash -c "source /opt/ros/indigo/setup.bash;source ~/YOUR/CATKIN/WORKSPACE/devel/setup.bash;/path/to/script.sh"
Icon=/if/you/want/one/icon.png
Name=rosapp