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

[Tim Booth]

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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Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
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