Rake vs. Thor for automation scripts?

Rake and Thor serve different purposes.

Rake is a general build script tool that is project-specific. In other words, you put your rakefile into your project folder and in your project's source control, and you can create, build and do other automation tasks that are specific to your project in that rakefile. Rake requires a rakefile to run.

Thor is a general purpose command line scripting tool that makes it very easy to re-use scripts across many projects and to do project setup, etc., like you are suggesting. Thor allows you to "install" an executable script that you can call from anywhere on your system, similar to calling "ruby", "gem" or "rake" command lines. However, Thor's scripts are more suited to general purpose, cross-application automation because the Thor script does not rely on a file sitting in your project-specific folder. A Thor script is the entire script, packed and installed for re-use anywhere.

Based on your stated needs, you are better off using Thor because you will be able to install your script in one location and have it work anywhere on your system. You will not be bound to where a Rake file is sitting or anything like that.

By the way, Rails 3 uses Thor for pretty much everything that is not project specific. You still have a Rake file and you still run things like "rake db:migrate" or "rake test:units". Thor is used for things like "rails new ...", "rails server" and "rails generate ..." The use of Thor AND Rake in Rails 3 is the perfect illustration of where each of these tools is best suited.

For setting up Ubuntu chores, Chef might be a better option.

From their web site:

Chef is an open source systems integration framework, built to bring the benefits of server configuration management to your entire infrastructure.

It's written in Ruby and there are tons of Chef recipes/cookbooks. Chef will handle setting up Ubuntu and installing packages, servers, etc.

I don't know if you are working with virtual machines, but Vagrant will set up a virtual machine and then use Chef to configure it.

There is something important to mention here.

http://guides.rubyonrails.org/generators.html in its section 8 Application Templates.

You can execute git commands, select gems, capify project.

And you could also execute system commands to satisfy your last point: Upgrade Ubuntu, install all basic packages through apt-get.