Setup for VirtualBox VM running Ubuntu 14.04 on OS X Mavericks
Fri 06 February 2015 — Filed under notes; tags: linux, mac, virtualboxTable of Contents
Here are my notes for setting up an Ubuntu VM to work on some web applications. This is intended to be a sandbox for development, so I'll err on the side of convenience (at the expense of security, since the VM should never be accessible from outside of the host machine). I'm doing this on a machine running OS X Mavericks. Much of the content was adapted from this really excellent post:
https://leemendelowitz.github.io/blog/ubuntu-server-virtualbox.html
I also went on to provide local network access via a static IP address. I chose not to include the guest additions or a shared directory - I wanted to interact with this VM as if it were a remote host.
VirtualBox preferences
Install VirtualBox from the vendor's website.
vboxmanage --version
4.3.20r96996
First, there are some application-level settings that should be modified right off the bat.
Rename the default location for VirtualBox resources to something sensible.
VirtualBox -> Preferences -> Default Machine Folder -> ~/VirtualBox
Create a host-only network. Go to
VirtualBox -> Preferences -> Network -> Host Only Networks
and from here, click on the little green icon with a plus on the right -
this creates the host-only network vboxnet0
. We'll need this later.
Create an Ubuntu 14.04 VM
Download ubuntu-14.04.1-server-amd64.iso here (we'll move it into $VBOXDIR below).
VBOXDIR="$HOME/VirtualBox" VM_NAME="Ubuntu14.04-1" UBUNTU_ISO_PATH="${VBOXDIR:?}/ubuntu-14.04.1-server-amd64.iso" VM_HD_PATH="${VBOXDIR:?}/${VM_NAME:?}.vdi" mkdir -p "${VBOXDIR:?}" mv ~/Downloads/ubuntu-14.04.1-server-amd64.iso "${VBOXDIR:?}"
Create the VM.
vboxmanage createvm --name ${VM_NAME:?} --ostype Ubuntu_64 --register
Virtual machine 'Ubuntu14.04-1' is created and registered. UUID: 58826a23-fceb-4a03-b7c3-cc22c975ccec Settings file: '/Users/nhoffman/VirtualBox/Ubuntu14.04-1/Ubuntu14.04-1.vbox'
I have to confess that I never could have figured these command out
without the post above. The ones defining HD and memory allocations
seemed pretty obvious. The last three lines will allow us to ssh into
the VM once the OS is installed (see below). If I could wish for one
thing from the VirtualBox application, it would be to generate the
corresponding vboxmanage
command from a menu action.
vboxmanage createhd --filename ${VM_HD_PATH:?} --size 12288 # size in MB (12GB) vboxmanage storagectl ${VM_NAME:?} --name "SATA Controller" --add sata --controller IntelAHCI vboxmanage storageattach ${VM_NAME:?} --storagectl "SATA Controller" --port 0 --device 0 --type hdd --medium ${VM_HD_PATH:?} vboxmanage storagectl ${VM_NAME:?} --name "IDE Controller" --add ide vboxmanage storageattach ${VM_NAME:?} --storagectl "IDE Controller" --port 0 --device 0 --type dvddrive --medium ${UBUNTU_ISO_PATH:?} vboxmanage modifyvm ${VM_NAME:?} --ioapic on vboxmanage modifyvm ${VM_NAME:?} --memory 1024 --vram 128 vboxmanage modifyvm ${VM_NAME:?} --nic1 nat vboxmanage modifyvm ${VM_NAME:?} --natpf1 "guestssh,tcp,,2222,,22" vboxmanage modifyvm ${VM_NAME:?} --natdnshostresolver1 on
Ok! This should result in a bootable VM. Here goes the first boot.
vboxmanage startvm ${VM_NAME:?}
Now we let Ubuntu install itself. I chose the default for each option and provided some extremely boring and insecure host settings:
- hostname: ubuntu
- full name: ubuntu
- username: ubuntu
- password: ubuntu
Obviously this would be a terrible idea for a real system (as are an ssh key without a passphrase, and allowing sudo without a password, both of which I will be guilty of below).
Once the system is installed, perform an upgrade and install the bare essentials that will allow us to ssh in.
sudo apt-get update && sudo apt-get -y upgrade sudo apt-get install -y openssh-server sudo shutdown -h now
This is a good time to make a snapshot ("clean-image"). From now on, I'll run the VM "headless" and ssh in to avoid having to use the horrible VirtualBox terminal.
vboxmanage startvm Ubuntu14.04-1 --type headless
For now, we can ssh in using port 2222 redirected to localhost, but in a minute, we'll give the VM an IP address.
ssh -p 2222 ubuntu@localhost
Now I'll degrade the security of my little VM sandbox even further by allowing the ubuntu user to sudo without a password. Edit the sudoers file:
sudo visudo
And add the following lines:
# ubuntu user can sudo without password ubuntu ALL= NOPASSWD: ALL
Set up an IP address
I pieced together the following with the help of the following posts:
- http://www.websightdesigns.com/posts/view/how-to-set-up-a-local-web-server-with-virtualbox-on-mac-os-x
- http://anupriti.blogspot.com/2014/10/invalid-settings-detected-virtualbox.html
- https://www.virtualbox.org/manual/ch06.html
First power off the VM.
vboxmanage controlvm Ubuntu14.04-1 poweroff
Now we need to create host-only network. I would have loved to know how to do this using vboxmanage. Go to the Setting for this VM:
Settings -> Network -> Adapter2 -> Enable Network Adapter
- Attached to: Host-only Adapter
- Name: vboxnet0
(remember, we created vboxnet0
in the application-level
configuration settings at the top).
Power the VM back on and ssh in as above, then modify
/etc/network/interfaces
as shown.
sudo -s cat >> /etc/network/interfaces <<EOF auto eth1 iface eth1 inet static address 192.168.56.101 netmask 255.255.255.0 EOF
After a restart, you should be able to ping the VM at 192.168.56.101
This should work, too:
ssh ubuntu@192.168.56.101
And if you run this from the VM
python -m SimpleHTTPServer
you should be able to point your browser to
http://192.168.56.101:8000
and see a directory listing of $HOME
!
Better yet, add an entry to /etc/hosts
on the host machine:
sudo -s cp /etc/hosts /etc/hosts.bak cat >> /etc/hosts <<EOF # for VirtualBox VM Ubuntu14.04-1 192.168.56.101 ubuntu1 EOF
and browse to the following address:
http://ubuntu1:8000
Now make a ssh key pair for this VM and install the public key.
cd ~/.ssh ssh-keygen -f vm-unsafe ssh ubuntu@192.168.56.101 'mkdir -p -m 700 ~/.ssh; cat - > ~/.ssh/authorized_keys; chmod 600 ~/.ssh/*' < ~/.ssh/vm-unsafe.pub
Finally, create an entry in ~/.ssh/config
(on the host machine, of
course) to create an alias for the VM:
Host ubuntu1 HostName 192.168.56.101 User ubuntu IdentityFile ~/.ssh/vm-unsafe
Now you can ssh in without a prompt for a password:
ssh ubuntu1
Time for another snapshot! ("ssh-ok")
That's enough for now. It kills me that there are so many manual steps in this process - more of them could probably be performed via the command line given more time and patience than I have at this point!
Compiling bcl2fastq v2.15 on Ubuntu 12.04 and 14.04
Table of Contents
Illumina provides a program for demultiplexing sequencing output
called bcl2fastq
. They get a gold star for releasing the source -
the downside is that they release binaries only for RHEL/CentOS, and
no build instructions for Ubuntu. So …