Preparing VirtualBox images: Difference between revisions

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   apt-get install localepurge zerofree
   apt-get install localepurge zerofree
   # I think we don't need these packages... saves around 300MB  
   # 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  
  apt-get install alpine
   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
   # wanna remove more? show packages by size: dpkg-query --show --showformat='${Package;-50}\t${Installed-Size}\n' | sort -k 2 -n
   # 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
   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:
Now install the genome browser:

Revision as of 13:55, 3 March 2014

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 install alpine 
 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 
 # 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/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

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>