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

[Cox, Michael J]

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
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev