Hi Tim,<div><br></div><div>Phew! That was good timing! No problem - I might not get a chance to install and test it until the weekend though - is that too slow?</div><div><br></div><div>Cheers</div><div><br></div><div>Mike<br>
<br><br><div class="gmail_quote">On Thu, Mar 1, 2012 at 16:51, 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 Mike,<br>
<br>
I was just about to release my new Qiime 1.4 package, so I added your<br>
patch this morning and I'm just waiting for the DEB to rebuild on<br>
Launchpad (I'm now using Launchpad for staging new packages):<br>
<br>
<a href="https://launchpad.net/~tbooth/+archive/ppa1/+sourcepub/2282287/+listing-archive-extra" target="_blank">https://launchpad.net/~tbooth/+archive/ppa1/+sourcepub/2282287/+listing-archive-extra</a><br>
<br>
Launchpad says it should queue up the 64-bit build in about 20 minutes<br>
(ie. by 5:30 today) so would you be able to test it for me before I put<br>
it on the main server?<br>
<br>
Cheers,<br>
<br>
TIM<br>
<div class="HOEnZb"><div class="h5"><br>
On Thu, 2012-03-01 at 09:22 +0000, Mike Cox wrote:<br>
> Hi Tim,<br>
><br>
><br>
> We came across a bug in all versions of AmpliconNoise in QIIME<br>
> recently (1.3 on Biolinux, 1.4 macqiime, 1.4 virtual boxes), where<br>
> primers were no longer being stripped from the output (inflating OTU<br>
> estimates and affecting ID particularly with redundant primers).<br>
><br>
><br>
> It has been fixed in the SVN version of QIIME 1.4 and I've fixed it<br>
> locally on my machine by<br>
> editing /usr/share/pyshared/qiime/workflow.py.<br>
> Previously:<br>
><br>
> cmd = 'Parse.pl '+bc_seqs[i]+' '+truncate_len+' < '+\<br>
><br>
> so that it reads:<br>
><br>
> cmd = 'Parse.pl '+bc_seqs[i]+one_primer+' '+truncate_len+' < '+\<br>
><br>
> and confirmed this works for the install.<br>
><br>
> I don't know whether it's worth updating the package to the SVN QIIME<br>
> 1.4 where the fix is incorporated, or waiting for version 1.5 to do<br>
> the update (I don't know what their planned release date is for that<br>
> one).<br>
><br>
> Cheers<br>
><br>
><br>
> Mike<br>
><br>
><br>
><br>
><br>
><br>
> blog: <a href="http://palecomic.tumblr.com/" target="_blank">http://palecomic.tumblr.com/</a><br>
> skype: mikeyjcox<br>
> twitter: mikeyj<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<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>
<a href="tel:%2B44%201491%2069%202705" value="+441491692705">+44 1491 69 2705</a><br>
<br>
--<br>
This message (and any attachments) is for the recipient only. NERC<br>
is subject to the Freedom of Information Act 2000 and the contents<br>
of this email and any reply you make may be disclosed by NERC unless<br>
it is exempt from release under the Act. Any material supplied to<br>
NERC may be stored in an electronic records management system.<br>
<br>
_______________________________________________<br>
Bio-Linux-dev mailing list<br>
<a href="mailto:Bio-Linux-dev@nebclists.nerc.ac.uk">Bio-Linux-dev@nebclists.nerc.ac.uk</a><br>
<a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev</a><br>
</font></span></blockquote></div><br></div>