[Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?

[Tony Travis]

On 20/01/16 18:01, Andor J Kiss wrote:
> Hello,
> 
> Does anyone know the future plans for Bio-Linux?  In terms of Bio-Linux
> 9 & Ubuntu 16.04 LTS?

Hi, Andor.

I've already volunteered to help keep the Bio-Linux project rolling, but
it is unclear what, if any, continuation of EOS/NEBC funding there might
be to continue supporting Bio-Linux development.

I think we should let Tim Booth lead the discussion about Bio-Linux 9
when he has settled into his new job in Edinburgh.

Meanwhile, we in the Bio-Linux community can continue to provide help
and support for people who want to use the existing Bio-Linux 8.

I've had good success using Tim's 'upgrade' script to create physical
and virtual Bio-Linux instances based on 'standard' Ubuntu 14.04 LTS:

> http://environmentalomics.org/bio-linux-installation/
> wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh

There are some minor problems with the script, but one show-stopper is
the way Tim's script checks if you have the 'multiverse' repository
enabled in Ubuntu 14.04 LTS. This is how I did it under OpenStack on
iPlant Atmosphere recently:

> http://www.iplantcollaborative.org/ci/atmosphere

> Upgrade Ubuntu 14.04.02 LTS base VM to Bio-Linux 8
> 
> # start Ubuntu 14.04.2 no GUI base VM and login
> ajtravis at vm64-212:~$ 
> sudo -i
> root at vm64-212:~# 
> 
> wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> chmod +x upgrade8.sh
> 
> # capture Bio-Linux 8 upgrade script
> vim upgrade8.sh
> ...
> #cd "`mktemp -d || echo /dev/null`"
> #if [ "$?" != 0 ] ; then
> #  echo "Unable to change to temporary directory; cannot continue."
> #  exit 2
> #fi
> ...
> ./upgrade8.sh |& tee upgrade8.log
> 
> # fix bug when upgrading 'Vanilla' Ubuntu 14.04
> vim upgrade_to_8.sh
> ...
> # If this was run on a Vanilla Ubuntu 14.04 box then Universe/Multiverse sources
> # will not be active.  Tell the user about it.
> if grep -qw universe   /etc/apt/sources.list && \
>    grep -qw multiverse /etc/apt/sources.list ; then
> ...
> 
> # remove conflicting packages
> apt remove gnome-bluetooth
> 
> # upgrade to Bio-Linux 8
> ./upgrade_to_8.sh |& tee upgrade_to_8.log
> ...
> Err http://archive.ubuntu.com/ubuntu/ trusty/universe prank amd64 0.0.140110-1
>   Could not resolve 'archive.ubuntu.com'
> E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/universe/p/prank/prank_0.0.140110-1_amd64.deb  Could not resolve 'archive.ubuntu.com'
> ...
> 
> # restart upgrade
> ./upgrade_to_8.sh
> 
> # ubuntu-desktop installed, but not dependencies
> apt remove ubuntu-desktop
> apt install ubuntu-desktop
> 
> # tidy up /root
> root at vm64-212:~# 
> logout
> ajtravis at vm64-212:~$ 
> sudo rm /root/*
> sudo rm /root/.bash_history
> sudo rm -r /root/.config
> sudo rm /root/.viminfo
> sudo ls -al /root
> total 20
> drwx------  3 root root 4096 Nov 25 08:50 .
> drwxr-xr-x 23 root root 4096 Nov 25 07:36 ..
> drwx------  2 root root 4096 Nov 25 08:26 .aptitude
> -rw-r--r--  1 root root 3106 Feb 19  2014 .bashrc
> -rw-r--r--  1 root root  140 Feb 19  2014 .profile


One way forward is for us to try modifying Tim's Bio-Linux 'upgrade'
script with a view to creating a Debian Bio-Linux meta-package like the
one for "ubuntu-desktop". This will not, of course, provide a new
Bio-Linux 9 'live' DVD, but it would allow us to identify problems and
make remastering an Ubuntu 16.04 LTS .iso image later on much easier.

Bye,

  Tony.

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