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

[Tim Booth]

Hi Mike,

See my reply to Tony.  I have Qiime 1.5 happily on my BL7 machine so you
should be able to get it on yours.  When I run "qiime print_qiime_config
-t" I get the following errors due to missing dependencies:

ParsInsert is missing
clearcut is missing
cluster_jobs_fp is missing
pplacer is missing
rtax is missing
usearch is missing *

You can install these manually if you need them.  If you want them
packaged up in a hurry you'll need to put in an NBAF application or bung
Tony some cash.

* in the case of USearch, unlike UClust, the license prohibits any
redistribution.

I also get the following errors but as far as I know these things
actually work fine, even though the version is unsupported:

R is unsupported version
BLAST is unsupported version
maptplotlib is unsupported version
mothur is unsupported version
numpy is unsupported version
python is unsupported version
raxmlHPC needs updating

Cheers,

TIM

On Wed, 2012-09-26 at 17:02 +0100, Cox, Michael J 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
> > 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
> 
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-- 
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