Re: Please check new version of tophat
Le Sat, Oct 04, 2014 at 10:30:30PM +0200, Andreas Tille a écrit :
>
> I tried to adapt the patches of the new version of tophat (2.0.13).
> While the package build it creates an extra executable which is
> installed to /usr/bin/samtools_0.1.18 which IMHO should be prevented.
> Since I'm not that deeply involved in tophat I wonder whether somebody
> else could test this new version since it is most probably what will
> end up in our next stable release.
Hi Andreas,
It is obviously a reaction to the replacement of libbam by the HTSlib in
Samtools 1.x, on which TopHat is built.
What puzzles me the most is that the authors did not take the final version of
the legacy Samtools (0.1.19) for their embeded code copy.
Here in Debian we do distribute the libbam via the samtools-legacy package, but
at its latest version, not 0.1.18.
Second problem, in this TopHat update, the authors removed the code for
providing libbam externally.
Altogether, our choices are:
- Extensive patching and risking to introduce bugs by overloking functions
that would work with libbam 0.1.18 but not 0.1.19. Let's not do this.
- Distribute Debian with tophat 2.0.12 and samtools 0.1.19 (still in Testing).
- Distribute tophat 2.0.13 with its embeded code copy.
Unfortunately, TopHat 2.0.13, from fresh downloaded upstream sources, fails to
build on my system. We might be forced to release with samtools 0.1.19 if this
problem is not solved (and I doubt I am able to solve it myself).
Have a nice Sunday,
Charles
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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