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

[Kelvin Jefford]

FYI ... You can change the desktop to whichever setting you like ...
Unity, Gnome 2, Gnome 3, XFCE, BlackBox ... etc. Might be a bit more
complex to change to KDE I'm sure, as the others use the nautilus
(gnome) desktop.

On the Ubuntu forums you should be able to find out the right info.

If you need help, I might be able to find the information for you.

Kelvin Jefford

On 26/09/2012, Cox, Michael J <mikeyj.cox at gmail.com> wrote:
> Exciting!
>
> Would QIIME 1.5 be included in the update or is that going to take some
> further fun and games after BL7 is a go?
>
> Cheers
>
> Mike
>
> @mikeyj
>
>
> On 26 Sep 2012, at 16:45, "Booth, Timothy G." <tbooth at ceh.ac.uk> wrote:
>
>> 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
>>
>> --
>> This message (and any attachments) is for the recipient only. NERC
>> is subject to the Freedom of Information Act 2000 and the contents
>> of this email and any reply you make may be disclosed by NERC unless
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>> NERC may be stored in an electronic records management system.
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>
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