Standard Debian install

hostname: neurodebian
domain: ''

all file in one partition

root: not there
user: brain
pwd: neurodebian


Do a minimal install
--------------------

All files in one partition/
just base system, run selection, but no tasks (not even 'Standard system')


install new stuff
-----------------

Add sources.list for backports and neurodebian
wget -O /etc/apt/sources.list.d/neuro.debian.net.list http://neuro.debian.net/_static/neurodebian.lenny.us.sources.list
echo "deb http://www.backports.org/debian lenny-backports main contrib non-free" >> /etc/apt/sources.list.d/backports.org.list
wget -O - http://backports.org/debian/archive.key | apt-key add -
wget -O - http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add -

install kernel 2.6.27 (or later) from backports to have support for OpenGL
direct rendering in VirtualBox
(and deinstall the old one, after a successfull reboot)

# a basic desktop
aptitude install \
 alacarte desktop-base evince file-roller gcalctool gdm gksu gnome-core
 gnome-keyring gnome-utils gnome-volume-manager gnome-mount gthumb
 bash-completion less mc gnome-themes etckeeper git-core gitk ntpdate
 alsa-utils

# install network manager applet
# but we don't want to have all the openvpn stuff that pull in an armada of
# things: I did it by hand in aptitude

# cleanup unwanted stuff
# video drivers (all but vesa)
aptitude purge $(apt-cache search --names-only --installed xserver-xorg-video | grep xserver-xorg-video | cut -d ' ' -f 1,1) xserver-xorg-video-vesa+
# random stuff
aptitude purge radeontool sound-juicer

# setup etckeeper
etckeeper init

# prepare for kernel module building (guest additions)
aptitude install module-assistant
module-assistant prepare
# note guest additions for 3.1.2 are broken, use 3.1.0
bash /media/cdrom/VBoxLinuxAdditions-amd64.run (need 2.6.27+ kernel for direct rendering)
#make sure that xorg.conf has 'vboxvideo' as device driver and also
echo "vboxvideo" >> /etc/modules

# make user brain allowed to execute sudo without a password
adduser brain sudo
visudo
# and uncomment the respective line at the end of the file
# (make sure there is nothing below it)

# configure shared folders
mkdir /mnt/host
mount -t vboxsf host /mnt/host
# better put the following into the session startup config of the user
# stupid wrapping into bash line to workaround a silly bug in Virtualbox additions
bash -c "cd /; sudo mount -t vboxsf -o defaults,uid=brain,gid=brain host /mnt/host"


# neuro-stuff
aptitude install afni afni-atlases amide caret dicomnifti fsl fsl-atlases lipsia
 minc-tools odin psychopy python-mvpa python-pyepl python-mvpa-doc

# general scientifically useful stuff
aptitude install ipython python-h5py vim-python

# next step purge network interface config to give the power to network manager
# important
adduser brain netdev


user config
-----------
# put use home dir in git to be able to track changes
git init

mkdir -p /home/brain/.config/backgrounds
cp /mnt/host/.config/awesome/hotbrain.png /home/brain/.config/backgrounds/

#change menu icon
sudo cp /mnt/host/hacking/neurodebian/artwork/icon.svg /usr/share/icons/Mist/scalable/places/start-here.svg


Deploy
------

# shrink VDI image by writting to a new (unfragmented) image
# target VDI needs to have proper partition table and MBR
# simplest solution: clonezilla

# clean up the master COPY
cp ~/vm/nd_master.vdi /tmp/nd_master.vdi
cd /tmp
mkdir -p vbdev vbmnt
# get access to disks inside the VDIs
sudo vdfuse -f nd_master.vdi vbdev
# mount partitition
sudo mount -o loop vbdev/Partition1 vbmnt

# remove cruft
# package cache
sudo find vbmnt/var/cache/apt/archives/ -name '*.deb' -delete
sudo rm vbmnt/var/cache/apt/*.bin
# device files -- udev restores them
sudo rm -rf vbmnt/dev/*
# tmp
sudo rm -rf vbmnt/tmp/*
# log files
sudo find vbmnt/var/log -type f -delete
# apt lists
sudo find vbmnt/var/lib/apt -type f -name '*debian*' -o -type f -name '*list*' -delete
# history
sudo rm vbmnt/root/.bash_history
sudo rm vbmnt/home/brain/.bash_history

# unmount filesystem
sudo umount vbmnt
# zero out empty space
sudo zerofree -v vbdev/Partition1
# close whole VDI
sudo umount vbdev

# compact VDI
# THIS NEEDS TO BE DONE ON A VDI THAT IS REGISTERED WITH VIRTUALBOX
VBoxManage modifyhd nd_master.vdi --compact