[Bio-linux-dev] Qiime 1.2.1

[Martin Ostrowski]

Hi Tim,

I think that I missed the window to download the qiime and pycogent packages. The server with those packages is not responding.

Thanks for your help with this package. After many headaches I got a partial build of Qiime 1.2.1 and dependencies going on my Mac server but there are a few Warwick people now asking me about additional functions.

We should be able to give it a good test this week.

Thanks again

Martin


On 25 Mar 2011, at 09:38, Tim Booth 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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