Could you please give more details? Jenkinks (or any other devops tool) doesn't really care are you calling bash, py or make scripts on the build machine. It just evaluates some code and returns you the status with logs
So currently what my jenkins is doing is checking out the repo, run the makefile which in terms runs the complete flow of the fpga. I have no problem doing these actions manually but somehow when jenkins runs the makefile on it's workspace, the fitter fails because it is saying that there is error of wrong atom placement (and no detail of this error)