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<div class="moz-cite-prefix">Hi Tim,<br>
<br>
Sounds great, please post to the list when you have the package
ready. In the meantime, I figured out a workaround to the problem:<br>
<ol>
<li>The installed version of tophat looks for the bowtie2
executable using the name "bowtie2-align" which only exists
for older versions of bowtie2. In newer versions of bowtie2,
the aligner is renamed just "bowtie2". The solution here is to
create a symbolic link "bowtie2-align" in /usr/bin that points
to the "bowtie2" wrapper script.</li>
<li>The other change necessary is a little worse to implement.
For this we actually need to hack the tophat python script as
detailed in this post:
<a class="moz-txt-link-freetext" href="https://groups.google.com/d/msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ">https://groups.google.com/d/msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ</a>.
Its only a one line addition to get tophat to get the sam
header from bowtie2 properly, specifically adding the -x
argument.</li>
</ol>
<p>These two changes got tophat working (mostly) properly with
bowtie2 with the default installed versions.<br>
</p>
<p>The thing that was weird for me was that running tophat with -p
> 3 would cause my entire system to become completely
unresponsive. I have a system with two quad-core processors so I
tried running with "-p 8", and the system would freeze (mouse
and keyboard did nothing). Running tophat with -p in {1, 2, 3}
worked very well, and saw appropriate speedups, but using any -p
>= 4, the system would freeze. Any ideas on this? This issue
seems quite weird to me. I have a post about it over on biostars
(<a class="moz-txt-link-freetext" href="https://www.biostars.org/p/122639/">https://www.biostars.org/p/122639/</a>)<br>
</p>
<p>Thanks,<br>
</p>
<p>Josh<br>
</p>
<pre class="moz-signature" cols="72">Josh Thackray
Laboratory Researcher III
Human Genetics Institute of NJ
Department of Genetics
Rutgers University</pre>
On 12/8/2014 7:00 AM, <a class="moz-txt-link-abbreviated" href="mailto:bio-linux-request@nebclists.nerc.ac.uk">bio-linux-request@nebclists.nerc.ac.uk</a>
wrote:<br>
</div>
<blockquote
cite="mid:mailman.1.1418040002.28888.bio-linux@nebclists.nerc.ac.uk"
type="cite">
<pre wrap="">Hi Josh,
I was looking at updating all the "Tuxedo Tools" packages at the end of
last week but due to some library interdependencies it's taking longer
than I expected. I don't want to risk making things worse by rushing
untested updates onto the main package repository.
However, if you still need a package for TopHat 2.0.13 then I've put one
here:
<a class="moz-txt-link-freetext" href="http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb">http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb</a>
If you download that and install it
(sudo dpkg -i tophat_2.0.13-0biolinux1_amd64.deb) then I'm hoping it
will fix your problem.
Cheers,
TIM
On Wed, 2014-12-03 at 17:20 +0000, Josh Thackray wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I am running biolinux 8 and am trying to use Tophat (version 2.0.9) but
this is incompatible with the version of bowtie2 (2.2.3) installed on
the system by default. It looks like this issue was resolved in tophat
version 2.0.12. It looks like the issue has to do with a change in the
structure of the bowtie2 package where the aligner changed names from
"bowtie2-align" to just "bowtie2". How can I update my tophat to this
version?
Thanks,
Josh
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
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