How to run a shell script at startup

The file you put in /etc/init.d/ have to be set to executable with:

chmod +x /etc/init.d/start_my_app

As pointed out by @meetamit, if it still does not run you might have to create a symbolic link to the file in /etc/rc.d/

ln -s /etc/init.d/start_my_app /etc/rc.d/

Please note that on the latest versions of Debian, this will not work as your script will have to be LSB compliant (provide at least the following actions: start, stop, restart, force-reload, and status): https://wiki.debian.org/LSBInitScripts

As a note, you should always use the absolute path to files in your scripts instead of the relative one, it may solve unexpected issues:

/var/myscripts/start_my_app

Finally, make sure that you included the shebang on top of the file:

#!/bin/sh

First create your startup script @ /home/user/startup.sh, and make it executable

chmod +x /home/user/startup.sh

Then set a crontab for it:

$ crontab -e
@reboot  /home/user/startup.sh

Now your your startup.sh script will run at every start.