To use this to build a new VM, follow these steps:

1. $ sudo ./vm_builder.sh
2. Configure Shared Folders (see shared folders below)
3. Configure Networking (see LSF section below)
4. $ sudo ./mount.sh $UID
    - The $UID arg is to allow your user to read the shared folders
      after they are mounted. If you intend to use LSF, ensure your
      UID is set via the instructions listed in the networking
      section.
5. $ ./user_script
6. $ source ~/.bashrc

Run these as root:
$ sudo ./vm_builder.sh

Configure Shared Folders
Configure Networking
$ sudo ./mount.sh

Run these as your user:
$ ./user_script.sh

Set up your environment
$ source ~/.bashrc

Shared Folders
---
Assuming you are using a Virtualbox VM at The Genome Institute,
you will need to add the following names and paths as shared folders:

name    path
---     ---
gscmnt  /gscmnt
lsf     /usr/local/lsf
var     /gsc/var

Before running the setup scripts above, you will need to ensure
the guest modules are installed on your test vm.

LSF / Networking
---
In order to use LSF at The Genome Institute,
the VM must have an IP accessible elsewhere on the network
and be added to the LSF cluster.

The mount.sh script will mount the /usr/local/lsf folder
and user_script.sh will configure the environment variables.

You will also need your VM to use a bridged network adapter,
and your VM must be appropriately configured with a static IP.

For example, my /etc/network/interfaces has a section like this:

auto eth#
iface eth# inet static
address 10.0.3.48
netmask 255.255.255.0
network 10.0.3.0
broadcast 10.0.3.255
gateway 10.0.3.253

If you are sure /usr/local/lsf is mounted and the various
lsf commands like bsub and bhosts are in your PATH, but you
receive permission errors, you likely need systems to add
your VM to the lsf cluster.

In order to dispatch to LSF, you must have the same username
and user number as on your workstation. In order to set the
user number, on your workstation run:

$ echo $UID

To see your user number. Then, on the VM, run:

$ sudo usermod -u (number from before) $USER