Preparing VirtualBox images

Start with a fresh Ubuntu 14.04 image, call the main user "browser".

 apt-get install localepurge zerofree
 # I think we don't need these packages... saves around 300MB 
 apt-get install alpine acpi-tools gpm 
 apt-get install libgomp1 # for rnaplot
 # which package contains the psxy tool?
 
 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 command-not-found alpine-doc python3.3-minimal apparmor linux-firmware
 # 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
 # consolkit keeps / open which is annoying for zerofill, acpi-tools doesn't really need I hope
 sudo dpkg -r --force-depends consolekit

Now install the genome browser:

 wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/installBrowser.sh
 sudo bash
 source installBrowser.sh

We need the guest extensions for shared folders:

on the virtualbox host attach the guest extension ISO from http://download.virtualbox.org/virtualbox/4.3.8/ (or rather try the most current version matching your Vbox):

 VBoxManage storageattach "browserbox" --storagectl "IDE Controller" --port 0 --device 0 --type hdd --medium "/cluster/home/qateam/VirtualBox VMs/VBoxGuestAdditions_4.3.8.iso"

on the guest:

 apt-get install linux-headers-3.13.0-24-generic build-essentials dkms  # replace 3.13.0-generic with your kernel version, show with uname -a
 mount -t iso9660 -o ro /dev/cdrom /mnt
 cd /mnt   
 ./VBoxLinuxAdditions.run
 modinfo vboxguest # check if they work
 # now to save some space, remove the kernel module build system 
 sudo apt-get remove build-essential linux-headers*
 apt-get clean
 apt-get autoremove # this should get rid of gcc, etc
 

The command to remove the ISO made me pull my hair out:

 VBoxManage storageattach "browserbox" --storagectl "IDE Controller" --port 0 --device 0 --type hdd --medium none

It's nice to have shared folders:

 sudo addgroup vboxsf
 sudo adduser browser vboxsf

Copy the various files from kent/src/browserbox to their respective locations. This is explained in kent/src/browserbox/README.txt. Some more details are in kent/src/browserbox/root/changes.txt

Ask Hiram to install the trash cleaner.

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

 sudo wget http://hgwdev.soe.ucsc.edu/~max/browserbox/cleanVm
 chmod a+x cleanVm
 sudo cleanVm

Zero the disk image:

 sudo /root/zeroVm # this unfortunately does not work. You need to reboot in single-user mode and run it as root there

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

 vboxmanage modifyhd –compact browserboxBoot.vdi
 vboxmanage modifyhd –compact browserboxData.vdi

• see [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 a disk that is still attached (e.g the guest install iso), 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>

the box release business is now automated with a script, in the qa user:

 boxRelease.sh