build_process_14.04.5.txt

Changelog:
    Build process:
        - Zsh exclusive commands now have a bash alternative listed under, all other commands can be executed in either bash or zsh.
        - Indentation for readability. This will not affect the copy/pasting of commands. In instances where it would it has been left out.        
        - Doesn't have to be run from an account called 'manager'
        - use of '~' has been replaced with $HOME
        - added [enter chroot] and [exit chroot] with separate indentation to clarify when to be in chroot
    Bio-Linux:
        - Updated Ubuntu base from 14.04.2 to 14.04.5
        - Optional local .deb to stop usb maker from overlapping partitions
        - Removed broken splash from liveUSB self checker
        - Forced liveUSB fat partition to mount read only so that it doesn't become corrupted when usb removed prematurely
        - Added the following programs:
            - mdadm
            - rkhunter
            - chkrootkit

Requirements:

    # Ubuntu >=14.04
    # Ubuntu 14.04.5 iso in home directory
    wget -c http://releases.ubuntu.com/trusty/ubuntu-14.04.5-desktop-amd64.iso

    # The following packages must be installed
    sudo apt install squashfs-tools

Build process:

1) Set up the build machine and unpack the ISO
2) Log into the ISO and make some changes
3) Install the master package list, as used by the upgrade8.sh script
4) Install a couple of extra things just for the ISO
5) Remaster and publish
6) Auto-build the .ova (with Packer) - not described here, see README    

1))) Initial unpacking.

    # commands marked with [zsh] have their [bash] equivalents below. Use 'echo $0' to check which one to use
    # Rename this git repo folder to Bl8bits if it isn't already -- many of the scripts rely on this
    # use a $HOME instead of ~. this should already be set to your home directory by linux
    echo $HOME
    # if this isn't set for some reason, set it with:
    HOME = '/home/username/'

    # Check the actual latest ISO at http://releases.ubuntu.com/trusty as the auto-download
    # URL no longer works


    #[zsh] 
    mkdir reconstructor && cd !#1
    #[bash] 
    mkdir reconstructor && cd reconstructor
     
    mkdir initrd remaster root original_cd_image

    sudo mkdir /mnt/cdrom1

    sudo mount -t auto -o loop $HOME/ubuntu-14.04*-desktop-amd64.iso /mnt/cdrom1

    rsync -av /mnt/cdrom1/ $HOME/reconstructor/remaster/

    chmod -R u+w remaster

    rsync -av /mnt/cdrom1/ $HOME/reconstructor/original_cd_image/

    chmod -R a-w original_cd_image

    sudo umount /mnt/cdrom1

    # Taken from 12.04 instruction
    cd ./initrd

    sudo bash -c "lzcat -Slz $HOME/reconstructor/remaster/casper/initrd.lz | cpio -i"

    # Unpack root fs
    cd ../root

    mkdir ../squashmount

    sudo mount -t squashfs -o loop,ro $HOME/reconstructor/remaster/casper/filesystem.squashfs ../squashmount/

    sudo rsync -av ../squashmount/ .

    sudo umount ../squashmount

    rmdir ../squashmount

2))) Non-packaged customisations

    # Review biolinuxfirstboot. Note this is checked by recon.test.d but not auto-fixed.
    sudo cp $HOME/bl8bits/biolinuxfirstboot $HOME/reconstructor/root/etc/init.d/

    #[zsh] 
    for rc in 1 2 ; sudo ln -s $HOME/reconstructor/root/etc/init.d/biolinuxfirstboot $HOME/reconstructor/root/etc/rc${rc}.d/S99biolinuxfirstboot
    #[bash]
    for rc in 1 2 ; do sudo ln -s $HOME/reconstructor/root/etc/init.d/biolinuxfirstboot $HOME/reconstructor/root/etc/rc$rc.d/S99biolinuxfirstboot; done

    # Everything else here should be at least checked by recon.test.d, and ideally fixed automagically.
    # Details about those changes are in the 14.04 build process.

3))) Packages

    # First do a regular dist-upgrade.

    sudo apt update && sudo apt dist-upgrade

    # [Enter chroot]
    ~/bl8bits/bin/openchroot

        apt-get update && apt-get dist-upgrade

        # Run
        apt-get autoremove --purge

    # [Exit chroot]

    # back up sources.list
    sudo cp $HOME/reconstructor/root/etc/apt/sources.list $HOME/reconstructor/root/etc/apt/sources.list.orig
    
    # activate the universe and multiverse
    sudo tee $HOME/reconstructor/root/etc/apt/sources.list < $HOME/bl8bits/sources.list 

    #Then run the upgrade_to_8 script. This will take some time, although requires user input partway through
    cp $HOME/bl8bits/upgrade_to_8/upgrade8.sh $HOME/reconstructor/root/tmp/ \
    && $HOME/bl8bits/bin/openchroot <<<'sh /tmp/upgrade8.sh'

    # /proc is busy so reboot before remastering
    # [OPTIONAL] move bio-linux-usb for install within chroot
    sudo cp $HOME/bl8bits/Bio-linux-usb-maker/bio-linux-usb-maker_8.2-2_all.deb $HOME/reconstructor/root/var/cache/apt/archives/

    # [Enter chroot]
    $HOME/bl8bits/bin/openchroot

        # Google patch. Needs all lines starting from cat up to and including EOT:
cat << EOT > /etc/apt/sources.list.d/google-chrome.list
### THIS FILE IS AUTOMATICALLY CONFIGURED ###
# You may comment out this entry, but any other modifications may be lost.
deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
EOT

    #apt upate may produce "W: There is no public key available for the following key IDs:", most likely for id 1397BC53640DB551 (which is for google). To resolve:
        sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1397BC53640DB551

        apt-get update

        apt-get install bio-linux-fixups

        #[OPTIONAL] install bio-linux-usb-maker within chroot
        dpkg -i /var/cache/apt/archives/bio-linux-usb-maker_8.2-2_all.deb

4))) Building the ISO

        # recon runs all the tests in recon.test.d, which can be hard to please. These are all the issues I encountered
        apt install exim4 ufw gufw

        # remove unwanted packages
        apt-get remove example-content aisleriot --auto-remove --purge

        # Purge any packages marked 'rc'
        sudo apt purge $(dpkg -l | awk '/^rc/{print $2}') 

        apt-get autoremove --purge
    
    # [Exit chroot]
    # remove wubi and autorun
    rm $HOME/reconstructor/remaster/wubi.exe $HOME/reconstructor/remaster/autorun.inf

    # Run recon script. This will need to be run a few times before it completes. 
    # replace 8.0.8 with an appropriate version number if necessary.
    ~/bl8bits/bin/recon 8.0.8