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

[Josh Thackray]

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
>>

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