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

Tim Booth tbooth at ceh.ac.uk
Fri Jun 27 07:49:18 EDT 2014

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.


    * 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 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 

+44 1491 69 2705

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