Re: Please check new version of tophat
Hi Dominique,
On Sun, Oct 05, 2014 at 09:12:13PM -0400, Dominique Belhachemi wrote:
> On Sun, Oct 5, 2014 at 7:59 PM, Charles Plessy <plessy@debian.org> wrote:
>
> > 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
> > > ----------------------------------------------------
Even if the discussion went further one remark: I think this is not the
correct attitude. If upstream had reasons to do a new release and is
shipping a copy of an older samtools version we should at least find out
the reasons for this since it might also mean that 2.0.12 is broken.
Do we have some connection to upstream to sort this out in a sensible
matter?
> I followed the 'Testing the installation' instructions on
> http://ccb.jhu.edu/software/tophat/tutorial.shtml .
>
>
> wget http://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz
> tar zxvf test_data.tar.gz
> cd test_data
> tophat -r 20 test_ref reads_1.fq reads_2.fq
>
>
> I am immediately running into the version parser issue.
>
> [2014-10-05 20:51:46] Beginning TopHat run (v2.0.12)
> -----------------------------------------------
> [2014-10-05 20:51:46] Checking for Bowtie
> Bowtie version: 2.2.3.0
> [2014-10-05 20:51:46] Checking for Samtools
> ...
>
>
> After a quick&dirty patch ...
>
> --- /usr/bin/tophat 2014-09-25 02:29:36.000000000 -0400
> +++ /usr/bin/tophat.patch 2014-10-05 20:45:55.900444000 -0400
> @@ -1537,10 +1537,10 @@
> samtools_out = proc.communicate()[1]
> ...
>
>
> I am getting the same results as with samtools 0.1.19:
>
> tophat -r 20 test_ref reads_1.fq reads_2.fq
>
> [2014-10-05 20:55:06] Beginning TopHat run (v2.0.12)
> -----------------------------------------------
> [2014-10-05 20:55:06] Checking for Bowtie
> Bowtie version: 2.2.3.0
> ...
> -----------------------------------------------
> [2014-10-05 20:55:07] A summary of the alignment counts can be found in
> ./tophat_out/align_summary.txt
>
>
> Any idea where to find upstreams test suite?
We definitely should contact upstream and we also should ship a test
suite. If there is no such thing as an upstream official development
test suite we should probably provide the test you did above (including
the test data) to enable autopkgtesting.
Kind regards
Andreas.
--
http://fam-tille.de
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