[Bio-linux-dev] java-6-openjdk

Tim Booth tbooth at ceh.ac.uk
Fri Aug 15 09:52:22 EDT 2014

Hi Tony,

This doesn't stop the script being idempotent, but I agree that its not
really designed to be run once the upgrade is done and you have started
reconfiguring things.

I judged that having programs run with the old Java, which triggers
nasty glitches, slowdowns and bugs in things like Artemis and Taverna,
was more of a risk than upsetting any things which really need Java 6,
but I may have been wrong so do keep me posted if you find further



On Fri, 2014-08-15 at 14:39 +0100, Tony Travis wrote:
> Hi, Tim.
> I just ran your 'indempotent' BL8 upgrade script again and realised that
> unconditionally purging "java-6-openjdk" might not be such a good idea
> after all...
> We need it to run the "Structure" GUI, which doesn't work properly with
> "java-7-openjdk":
>   http://pritchardlab.stanford.edu/structure.html
> I think there might be other programs that need java-6 too. I'll let you
> know about any problems I encounter. BTW, I've left java-7 as the
> default Java - I only use java-6 for particular programs that need it,
> by specifying the full path to java-6 in a wrapper script.
> Bye,
>   Tony.
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
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Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

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