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

[Tim Booth]

...continued from post to bio-linux-list

Regarding the upgrade script, yes please contribute fixes!

There's no need to go ferreting around to find the code, as it's all on
GitHub.  Fork it, patch it, test it, submit bugs, send pull requests,
etc.  It's all good!

https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8

Note that I don't any longer have access to the nebc.nerc.ac.uk server
that hosts some of the Bio-Linux static files like this script, but I
can edit content on environmentalomis.org and I have full control of the
Luanchpad and GitHub accounts.

TIM

On Wed, Jan 20, 2016, at 10:55 PM, Tony Travis wrote:
> 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.
> 
> -- 
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
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-- 
Of course I'm a technophobe; I program computers for a living!