Just append the path in the $PATH Variable in .bashrc like below:
export PATH=$PATH:/home/user/Project/sub1/sub2/sub3
And execute it from wherever you want in even without ./
$ ninja
But ofcourse you can set alias also
alias runNinja='/home/user/Project/sub1/sub2/sub3/ninja'
And execute from wherever:
$ runNinja
If you deliberately wanted to be in that directory when running this ( Ex:if you are processing any file as input/output from that directory or dependency) , you have to write a function like below in your ~/.bashrc file or profile:
runNinja() { cd /home/user/Project/sub1/sub2/sub3 && ./ninja "$@" }