[Bio-Linux] Qiime

[Alec Colebrook-Clark]

Hi Tony and Tim,

Thanks for the reply. I appear to and solved the problem by using the QIIME deploy for version 1.8 and then manually installed the USEARCH to get all dependencies to pass the test. It was a headache and I much prefer the APT way of installing it! 

Thanks
Alec

-----Original Message-----
From: Tony Travis [mailto:tony.travis at abdn.ac.uk] 
Sent: 12 September 2014 21:41
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Qiime

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


The University of Aberdeen is a charity registered in Scotland, No SC013683.
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