[Bio-linux-dev] Bio-Linux 8 ISO ready for Beta-testing

[Tim Booth]

Dear Devs,

I hit a few unexpected glitches making the new Bio-Linux 8 ISO,
particularly due to the way the keyboard layouts are handled in the new
Ubuntu (a total mess!) and to various other unexpected changes under the
hood of the system.  I also wanted to ensure I could release both .ISO
and .OVA versions at the same time.  The OVA is auto-built from the ISO
using the fantastic Packer tool so from now on it should always be
completely in sync.

I've now put a beta version (8.0.1-beta) up on
http://nebc.nerc.ac.uk/downloads/

Aside from a few cosmetic fixes, this is final and I expect to put up a
final 8.0.2 early next week and to announce it to the world along with
the new web content.  In particular, if you were to install from this
-beta image I can promise you will not have to re-install as all further
fixes will be handled via package updates.

The upgrade script described below has now been tested by several people
and glitches fixed, so I'm considering it final and will announce it
along with the ISO next week.

Release errata for 8.0.1-beta:

* The bioinformatics menu on the Dash still doesn't work, but once I fix
it I'll put out a package update and it will start working.
* Booting directly from USB with persistence enabled seems slow.  I'm
working to see if I can speed this up.  Once booted it's usable.
* There may still be some issues with keyboard setup.  Once you have the
system installed and you make an account you can set it up no problem.
* The OVA needs more testing and may not work yet on VMWare or
Parallels.
* I've not credited the new background images properly.  I'm rectifying
this right now!

Have a good weekend!

TIM

On Fri, 2014-06-27 at 12:49 +0100, Tim Booth wrote:
> Dear Bio-Linux-Dev subscribers,
> 
> It took longer than I planned, but I'm pleased to announce that the
> Bio-Linux 8 upgrade script (aka update to Ubuntu Trusty 14.04) is now
> available for testing.  I have tried the script out on several machines
> here including my own, and nothing has blown up (much).  However, as
> with any major upgrade you should be sure you have a reliable backup
> before proceeding.  And as with any beta test you should be prepared for
> glitches, so don't run the upgrade 2 hours before you need your machine
> for some critical analysis!  Please discuss any problems on this list
> and I will endeavour to respond helpfully as quickly as I can.
> 
> Notes:
> 
>     * There is no ISO or OVA download yet, so you can't test
>       installing Bio-Linux 8 from scratch or running a "Live" boot.
>       This is coming!
>     * The bioinformatics menu in the Dash doesn't work, due to fundamental
>       changes to the way this actually works under the hood.  You can still
>       search for tools but you can't just get a nice list of bioinf stuff
>       - I'm working on this. Switch to MATE desktop to get a working
>       bioinformatics menu (see below).
>     * You should be able to run the script on a vanilla Ubuntu 14.04 box to
>       Bio-Linux-ify it (minus a few things like default firewall
>       settings and sudo/ssh/postgresql config)
>     * All the bioinf packages have been updated for the new release, 
>       but testing is still ongoing so there may be issues
>     * None of the docs and tutorials are updated yet, but things are
>       broadly unchanged so experienced user shouldn't be baffled.
>     * NX is nixed, and x2go is go for remote desktops! Please test
>       this and let me know what you think.  The lightweight MATE
>       desktop is provided as it works well with x2go.
>     * You should see one of a selection of lovely new desktop
>       wallpapers.  I will credit the submitters of those on the
>       website when the other release material goes up.
> 
> To actually do the upgrade:
> 
> sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> 
> (or if the runurl command isn't found, just download the script and do
> "sudo sh upgrade8.sh" ).
> 
> Enjoy, and let me know how you get on.
> 
> 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