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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
