Preparing VirtualBox images

Start with a fresh Ubuntu 13.04 image, call the main user "browser".

 apt-get install localepurge zerofree
 # I think we don't need these packages... saves around 300MB 
 apt-get remove python3* linux-headers* aptitude man-db perl perl-modules geoip-database language-pack-gnome-en-base manpages ppp acpi iso-codes console-setup dmidecode eject ethtool initramfs-tools pciutils usbutils 
 # wanna remove more? show packages by size: dpkg-query --show --showformat='${Package;-50}\t${Installed-Size}\n' | sort -k 2 -n
 apt-get install apache2 mysql-server mysql-client

Now install the genome browser:

 wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/ubuntu.sh
 source ubuntu.sh

It's nice to have shared folders:

 sudo addgroup vboxsf
 sufo adduser browser vboxsf
 sudo wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/rc.local -O /etc/rc.local

Once you're finished with everything ubuntu related, you can free 120 MB:

 rm -f /var/lib/apt/lists/*

Now compact the disk image: reboot, press shift on boot, selected advanced, repair mode, root shell (different than telinit 1?):

  mount -o remount,ro /
  zerofree -v /dev/sda1

To show the IP address on startup, only necessary in bridged mode:

 sudo wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/show-ip-address -O /etc/network/if-up.d/show-ip-address
 sudo chmod a+x /etc/network/if-up.d/show-ip-address

Leave VirtualBox, shutdown the VM, go to a command line on the host, find the .VDI file and compact it:

 vboxmanage modifyhd –compact browserbox.vdi

• [Shrink the disk]

Have a quick look into the .vbox file and make sure that it doesn't list any iso images or other disk images that you attached once to the disk but don't need anymore. They trigger error messages on new host machines.

If you see one, get its UUID first:

 VBoxManage list hdds
 VBoxManage list dvd

The remove it:

 VBoxManage closemedium disk <paste uuid here>

or

 VBoxManage closemedium dvd <paste uuid here>