[Debian-med-packaging] Bug#780816: December: tophat

[Andreas Tille]

Hi Fabian,

thanks for working on this.

On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote:
> I just pushed some changes to build tophat with our version of libbam.
> Not sure if the previously mentioned issue in [1] is fixed; can't test,

Thanks to the test suite we now know that the issue is not solved yet:

$ sh run-unit-test 

[2017-12-04 17:28:54] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2017-12-04 17:28:54] Checking for Bowtie
                  Bowtie version:        2.3.3.1
Error locating program: samtools_0.1.18


Unfortunately a grep for this explicite string has several hits.  I
have no idea what might happen if we replace it by /usr/bin/samtools.

Kind regards

      Andreas.

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