Merge branch 'master' of github.com:dmlond/arangs2015

Author: dmlond

docs/2015-05-13/README.md

@@ -44,14 +44,19 @@ Schedule
 The outline for today is as follows:
 
 - _Session 1_: Recap from yesterday: How Vagrant and Puppet can automate the creation and
-configuration of compute environments and how to run analyses inside a VM. Brief
+configuration of compute environments and how to run analyses inside a VM. To capture our
+understanding of yesterday's progress, we will each make a mindmap with XMind. Give it a 
+name that includes your computer (t1, t2, etc.), add the file to your git repository and 
+send us a pull request. This way we have all of them together. Then we will have a brief
 aside on how to organize data, e.g. as produced by different runs of a pipeline or
 different steps in a larger analysis.
-- _Session 2_: If all has gone well, we will be able to access the folder
-`arangs2015/data` on the host by navigating to `/vagrant_data/` on the VM. Verify that
-this is the case and that you can read from it (e.g. by accessing the README.md using
-`more`) as well as write to it (e.g. `touch foo` should create an empty file `foo`).
-Modify the pipeline shell script to point it to the right folder and run it.
+- _Session 2_: We are going to make our own vagrant box file to share with others. The end
+result will be something [like this](https://atlas.hashicorp.com/Naturalis/boxes/arangs2015),
+which you can install with `vagrant init Naturalis/arangs2015` (etc.). A box file
+is [a combination of the virtual hard drive of the VM and metadata](http://docs.vagrantup.com/v2/boxes/format.html).
+This bundling is made using the [packer program](https://packer.io/), which you should install.
+The bundler requires some extra scripts and config files, which we will adapt from
+[here](https://github.com/hashicorp/atlas-packer-vagrant-tutorial).
 - _Session 3_: Docker introduction. We will now begin to look at a newer technology that has emerged within the last few years, Docker.  In this session,
 we will go over the basic concepts of the Docker system, and get to know its
 similarities and differences with Virtualization.  We will then learn about the docker ecosystem on registry.docker.hub. We will then install the