[Bio-linux-dev] Qiime 1.2.1

[Tim Booth]

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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