[Bio-linux-dev] Qiime 1.2.1

[Mike Cox]

Tim,

We love you.  I'll try this out as soon as possible and get back to you with
any problems.

Thanks

Mike

   Mike Cox


Research Associate

Centre for Respiratory Infection

National Heart Lung Institute

Royal Brompton Campus

Guy Scadding Building

London SW3 6LY


michael.cox1 at imperial.ac.uk

http://www1.imperial.ac.uk/medicine/people/michael.cox1/


On Fri, Mar 25, 2011 at 09:38, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi All,
>
> As promised, I'm currently working on the Qiime repackaging for 1.2.1.
> The Qiime package itself is rather small but has many dependencies and
> there are what cause all the aggro.  I know there are further updates
> needed but
> in the meantime, I've started by re-rolling the Qiime package.
>
> If you are able to try this in the next couple of days and let me know
> what does/doesn't work I'll try to fix things as fast as I can.  I'm
> also doing my own testing here and hopefully by early next week I'll
> have all the results in the package repository for a one-click install.
>
> As the package currently is half-baked, the instructions to install are
> a bit longer than the usual 'apt-get install bio-linux-qiime'...
>
> Instructions:
>
> 1)
> sudo apt-get remove bio-linux-qiime
>
>  # This will report that you do not need various packages any more -
>  # ignore this - you DO still need them.
>
> 2)
> wget
> http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb
> wget
> http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb
>
> 3)
> sudo dpkg -i qiime_1.2.1-ubuntu4_all.deb
> sudo dpkg -i python-cogent_1.5-2_amd64.deb
>
> 4)
> Grab uclustq1.2.21_i86linux64 from
> http://www.drive5.com/uclust/downloads1_2_21q.html
>
> sudo cp uclustq1.2.21_i86linux64 /usr/local/bin/uclust
> sudo chmod a+rx /usr/local/bin/uclust
>
> 5)
> As before, type 'qiime' to get into the qiime shell.  Alternatively you can
> now also
> invoke a single Qiime command like so:
>
> qiime check_id_map [...]
>
> Cheers,
>
> 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
>
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