[Bio-Linux] Qiime

[Tony Travis]

On 12/09/14 15:06, Tim Booth wrote:
> Hi Alec,
>
> The QIIME quick self-test you get with "print_qiime_config.py -t" always
> gives some errors and probably always will because of the way it is set
> up.  I verify the QIIME installation with the more comprehensive
> regression tests rather than trying to match all the exact software
> versions they suggest.  So yes, QIIME seems to work fine with the newer
> (actually over a year old) FastTree even though it complains about the
> version.
>
> On the second question - If I knew a truly easy way to install QIIME I
> wouldn't have gone to all the trouble packaging it for APT!  More
> seriously, I would use their VirtualBox version if possible, because
> gathering all the old versions of tools needed for the old QIIME will be
> hard work.

Hi, Tim.

I, sort of, disagree with you about all this because QIIME is validated
against specific versions of tools and I installed them all by hand to
get it to pass its own tests. That is not, of course, consistent with
the spirit of Bio-Linux/Debian-Med packaging of software...

QIIME looks like an absolute perfect use-case example for Docker!

Instead of using VirtualBox to provide the specific environment that
QIIME is validated against, as an alternative we could encapsulate it in
a Docker container and run it under Bio-linux (or whatever OS).

What do you think?

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


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