Tim,<div><br></div><div>We love you. I'll try this out as soon as possible and get back to you with any problems. </div><div><br></div><div>Thanks</div><div><br></div><div>Mike</div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<p class="p1">Mike Cox</p>
<p class="p2"><br></p>
<p class="p1">Research Associate</p>
<p class="p1">Centre for Respiratory Infection</p>
<p class="p1">National Heart Lung Institute</p>
<p class="p1">Royal Brompton Campus</p>
<p class="p1">Guy Scadding Building</p>
<p class="p3"><span class="s1">London</span> SW3 6LY</p>
<p class="p4"><br></p>
<p class="p5"><a href="mailto:michael.cox1@imperial.ac.uk">michael.cox1@imperial.ac.uk</a></p>
<p class="p6"><span class="s2"><a href="http://www1.imperial.ac.uk/medicine/people/michael.cox1/">http://www1.imperial.ac.uk/medicine/people/michael.cox1/</a></span></p>
<br><br><div class="gmail_quote">On Fri, Mar 25, 2011 at 09:38, Tim Booth <span dir="ltr"><<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi All,<br>
<br>
As promised, I'm currently working on the Qiime repackaging for 1.2.1.<br>
The Qiime package itself is rather small but has many dependencies and<br>
there are what cause all the aggro. I know there are further updates needed but<br>
in the meantime, I've started by re-rolling the Qiime package.<br>
<br>
If you are able to try this in the next couple of days and let me know<br>
what does/doesn't work I'll try to fix things as fast as I can. I'm<br>
also doing my own testing here and hopefully by early next week I'll<br>
have all the results in the package repository for a one-click install.<br>
<br>
As the package currently is half-baked, the instructions to install are<br>
a bit longer than the usual 'apt-get install bio-linux-qiime'...<br>
<br>
Instructions:<br>
<br>
1)<br>
sudo apt-get remove bio-linux-qiime<br>
<br>
# This will report that you do not need various packages any more -<br>
# ignore this - you DO still need them.<br>
<br>
2)<br>
wget <a href="http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb" target="_blank">http://nebc.nerc.ac.uk/downloads/qiime_beta_test/qiime_1.2.1-ubuntu4_all.deb</a><br>
wget <a href="http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb" target="_blank">http://nebc.nerc.ac.uk/downloads/qiime_beta_test/python-cogent_1.5-2_amd64.deb</a><br>
<br>
3)<br>
sudo dpkg -i qiime_1.2.1-ubuntu4_all.deb<br>
sudo dpkg -i python-cogent_1.5-2_amd64.deb<br>
<br>
4)<br>
Grab uclustq1.2.21_i86linux64 from <a href="http://www.drive5.com/uclust/downloads1_2_21q.html" target="_blank">http://www.drive5.com/uclust/downloads1_2_21q.html</a><br>
<br>
sudo cp uclustq1.2.21_i86linux64 /usr/local/bin/uclust<br>
sudo chmod a+rx /usr/local/bin/uclust<br>
<br>
5)<br>
As before, type 'qiime' to get into the qiime shell. Alternatively you can now also<br>
invoke a single Qiime command like so:<br>
<br>
qiime check_id_map [...]<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
<br>
<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://nebc.nerc.ac.uk" target="_blank">http://nebc.nerc.ac.uk</a><br>
+44 1491 69 2705<br>
<br>
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</blockquote></div><br></div>