[Bio-Linux] biolinux 8, Tophat incompatible with Bowtie2

[Tim Booth]

Hi All,

I've now updated tophat, bowtie, bowtie2 and cufflinks on Bio-Linux.
The new packages will be installed via the update manager as usual.

This time I tested Tophat as described here:
http://ccb.jhu.edu/software/tophat/tutorial.shtml#test

With the old packages if I run this it says there is no bowtie2.  Now it
finds and uses it, so I'm taking this to mean it all works, but if you
find there are still issues please let me know.

Regarding TopHat freezing with -p >= 4, I'm really not sure.  Sometimes
if you increase the threads too much in a data-centric application you
can overwhelm the IO bus which freezes things up badly unless you have a
server-grade machine with SCSI disks.  Any chance things have improved
with the new packages?

Cheers,

TIM

On Mon, 2014-12-08 at 19:19 +0000, Josh Thackray wrote:
> Hi Tim,
> 
> Sounds great, please post to the list when you have the package ready.
> In the meantime, I figured out a workaround to the problem:
>      1. 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.
>      2. 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:
>         https://groups.google.com/d/msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ. Its only a one line addition to get tophat to get the sam header from bowtie2 properly, specifically adding the -x argument.
> 
> These two changes got tophat working (mostly) properly with bowtie2
> with the default installed versions.
> 
> 
> 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 (https://www.biostars.org/p/122639/)
> 
> 
> Thanks,
> 
> 
> Josh
> 
> 
> Josh Thackray
> Laboratory Researcher III
> Human Genetics Institute of NJ
> Department of Genetics
> Rutgers University
> On 12/8/2014 7:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
> 
> > 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:
> > 
> > http://nebc.nerc.ac.uk/downloads/bl8_only/tophat_2.0.13-0biolinux1_amd64.deb
> > 
> > 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:
> > > 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
> > > 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
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