I use this script to run commands over SSH in a new Vagrant machine to setup my own dotfiles.

up.sh

#!/bin/bash
vagrant up
vagrant ssh << EOF

# If directory doesn't exist, clone the repository in ~/.dotfiles
if [ ! -d ~/.dotfiles ];
then
	git clone --recursive https://github.com/coenjacobs/dotfiles.git ~/.dotfiles
fi

# Check if zsh is already installed
if ! dpkg-query -l zsh | grep -q ^.i
then
	sudo apt-get update && sudo apt-get -y install zsh
fi

# Check for line in .profile that makes zsh default shell
if ! grep -Fxq "[ -f /usr/bin/zsh ] && exec /usr/bin/zsh -l" ~/.profile
then
	echo "[ -f /usr/bin/zsh ] && exec /usr/bin/zsh -l" >> ~/.profile
fi

# Run install file inside dotfiles repository
sh ~/.dotfiles/scripts/install.sh

EOF