Preparing VirtualBox images: Difference between revisions
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Start with a fresh Ubuntu | Start with a fresh Ubuntu 14.04 image, call the main user "browser". | ||
apt-get install localepurge zerofree | apt-get install localepurge zerofree | ||
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# which package contains the psxy tool? | # 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 | 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 | # 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 | ||
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Now install the genome browser: | Now install the genome browser: | ||
wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/ | wget http://hgwdev.soe.ucsc.edu/~max/gbInstall/installBrowser.sh | ||
sudo bash | sudo bash | ||
source | source installBrowser.sh | ||
We need the guest extensions for shared folders: | We need the guest extensions for shared folders: | ||
on the host: | 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" | VBoxManage storageattach "browserbox" --storagectl "IDE Controller" --port 0 --device 0 --type hdd --medium "/cluster/home/qateam/VirtualBox VMs/VBoxGuestAdditions_4.3.8.iso" | ||
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./VBoxLinuxAdditions.run | ./VBoxLinuxAdditions.run | ||
modinfo vboxguest # check if they work | modinfo vboxguest # check if they work | ||
# now save some space, remove the kernel module build system | # now to save some space, remove the kernel module build system | ||
sudo apt-get remove build-essential linux-headers* | sudo apt-get remove build-essential linux-headers* | ||
apt-get clean | apt-get clean | ||
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sudo addgroup vboxsf | sudo addgroup vboxsf | ||
sudo adduser browser 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: | Once you're finished with everything ubuntu related, you can free 120 MB: | ||
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sudo 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 | 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: | Leave VirtualBox, shutdown the VM, go to a command line on the host, find the .VDI or VMDK file(s) and compact it: | ||
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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. | 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 | If you see a disk that is still attached (e.g the guest install iso), get its UUID first: | ||
VBoxManage list hdds | VBoxManage list hdds | ||
VBoxManage list dvd | VBoxManage list dvd | ||
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VBoxManage closemedium dvd <paste uuid here> | VBoxManage closemedium dvd <paste uuid here> | ||
the box release business is now automated with a script, in the qa user: | |||
boxRelease.sh | boxRelease.sh | ||
Revision as of 10:41, 6 October 2014
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
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
