Preparing VirtualBox images
This is part of the Genome_Browser_in_a_box_config
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
On the host again (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
On the guest again - 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
very obscure settings in gbib
https://www.virtualbox.org/ticket/12441
On the host:
vboxmanage modifyvm browserbox --natdnsproxy1 on vboxmanage modifyvm browserbox --natdnshostresolver1 on
This makes sure that the VM network works after you sleep your laptop on OSX or you change the wifi connection.
in /etc/rc.local
echo 180 > /sys/block/sda/device/timeout echo 180 > /sys/block/sdb/device/timeout
This tells the linux kernel to accept longer delays when writing to disk. If your host OS is busy during an rsync job, it will fail without these settings.
a2dismod deflate
This means that hgMirror can show its status message right away, it deactivates some buffering in apache on stdout.
