[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Booth, Timothy G.]

Dear Bio-Linux testers,

My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little
later than I first anticipated, but I have now finished all the package
updates and tested upgrading several machines in-house.  As far as I'm
aware, once you get through the upgrade, everything works and is ready
to use.  There is no ISO download just yet, but I invite everyone on
this list to try upgrading their Bio-Linux 6 systems in-place.  This is
the first time in 7 releases that we've been confident to advise
upgrading in-place without reinstalling.

In short, the upgrade process is fairly complex so I've prepared a
script to do all the necessary actions and make it simple for you.  If
the script doesn't finish for some reason you can simply run it again as
many times as you need to.  I've fixed all the issues I know about but
you may hit other problems - please report and discuss bugs on this
list, or even better file a bug report here:

https://bugs.launchpad.net/bio-linux

*** It should go without saying - don't do this on a critical server
just now.  Check you have a few GB free disk space before you start.
Back up your data first.  Really, back up your data first. ***

To run the script:

1) Open a terminal
2) download (using wget or otherwise) this script:
http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh
3) Run the script:
sudo bash ./bl_do_update_to7.sh

This will trigger everything off.  The script is designed to be run on a
Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu
12.04 box (or even on regular Ubuntu 10.04) as it first ensures that
Ubuntu is upgraded, then installs all the BL stuff, and finally clears
up some legacy packages and sets the backdrop.  If the new backdrop
doesn't appear you probably need to re-run the script again until it
does, or until you hit a bug that stops it working.

It will take about 2-3 hours to do the full upgrade.  You'll
periodically need to answer various questions that pop up.

Notes and known issues:

The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have
additional software sources (eg. PPAs) enabled.  You may need to disable
these via the "Additional Software Sources" tab in the update manager.
The CRAN repositories, FreeNX PPA, and the Google Chrome repository
(which is added automatically if you install Chrome) should be OK and
the upgrade script deals with them explicitly.

The Ubuntu upgrade also produces various warnings, and you may well see
a bizarre error box saying "☐☐☐☐ ☐☐☐☐☐☐☐☐ ☐☐☐☐ ☐☐☐☐".  You don't have to
worry about this!  There's not much I can do about these things as they
come from the core Ubuntu packages.

I think I've solved the errors where APT would complain about installing
unauthenticated packages, but if you see any such errors please let me
know.

Bio-Linux packages are split between the old repository (on
nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad.  You'll notice
some packages that can't go on Launchpad but don't work on BL6 will be
downloaded and installed separately.  This is a temporary workaround.

After upgrading you'll be using the Unity desktop.  This is going to be
the default on Bio-Linux 7 as it is the default on Ubuntu.  If you don't
like it and want to contribute instructions for swapping to
Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website,
but personally I'm sticking with Unity.  It's not so bad once you get
used to it!

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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