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]