Re: Please check new version of tophat
Le Sun, Oct 05, 2014 at 01:21:57PM -0400, Dominique Belhachemi a écrit :
>
> Based on the changelog I would say that you can skip the 2.0.13 release.
>
> ----------------------------------------------------
> TopHat 2.0.13 release 10/2/2014
> Version 2.0.13 is a maintenance release with the following changes:
>
> removed SAMtools as an external dependency in order to avoid
> incompatibility issues with recent and future changes of SAMtools and its
> code library (an older, stable SAMtools version is now packaged with
> TopHat)
>
> fixed a few code compatibility issues when compiling on OSX 10.9
> ----------------------------------------------------
>
> I wonder which versions of tophat/samtools are incompatible and why?
Hi Dominique,
You can see some reports in the following threads:
- https://www.biostars.org/p/112749/
- https://groups.google.com/forum/#!topic/tuxedo-tools-users/BVNDDmInU0A
If it were just the parsing of Samtool's version number, the solution would be
trivial, but I worry that TopHat may also be broken by changes in the default
output of Samtools. I think that if we would patch TopHat 2.0.12, we would
need to rely on somebody doing extensive tests. On my side, I am a BWA user…
Are there TopHat users here who could help us testing the possible alternatives ?
Cheers,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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