[Debian-med-packaging] picard-tools and htsjdk

[Andreas Tille]

Hi Vincent,

On Sun, Nov 06, 2016 at 07:28:11PM +0100, Andreas Tille wrote:
> Hi Vincent,
> 
> On Sun, Nov 06, 2016 at 11:56:28AM +0100, Vincent Danjean wrote:
> >   I just saw that picard-tools 2.7.1+dfsg-1 has been uploaded (it is
> > even in testing now). But I noticed two things:
> > 1) there is no depends on libhtsjdk-java (whereas the jar is in the
> >    classpath)
> 
> Just fix it and upload. :-)

Currently  picard-tools remains at 2.7.1+dfsg-1.  Feel free to ping me
if you have some time constraints ...

Kind regards

       Andreas.

> > 2) the htsjdk source package is still at 2.6.1+dfsg-1 in the archive
> >    (upstream released the 2.7.0 version)
> 
> At the time when I realised picard-tools 2.7.0 there was no version bump
> of htsjdk.  (I was explicitly checking for this.)
> 
> > A few time ago, picard-tools has been spit (upstream) in picard-tools
> > and htsjdk. For a while, upstream released both project at the same
> > time with the same version number (and expected that users also used
> > the same version for the two software).
> >   It seems that this latter requirement is now reduced (there is no
> > 2.7.1 release for htsjdk) but I ask myself if the major part of the
> > version number should be the same or not (I just asked the question to
> > upstream [1]).
> 
> I think we should release the latest htsjdk in any case.
>  
> >   So, for 1, the dependency must be added. The question is whether
> > this should be done with a minimal (and maximal ?) version or not,
> > ie "Depends: libhtsjdk-java (>= 2.7), libhtsjdk-java (<< 2.8)"
> 
> I personally have no competence to decide whether also the maximum
> limitation is needed.  I had the impression that this is not the case
> since the test suite was passing.
> 
> > If this is the case, it will be better to generate this automatically
> > to avoid not updating this for new versions...
> >   Or, perhaps, we should use virtual packages. Ie:
> > libhtsjdk-java: Provides: libhtsjdk-2.7-java
> > picard-tools: Depends: libhtsjdk-2.7-java
> >   What do you think? I can manage this once we decide what to do.
> 
> Thanks for volunteering to implement this.  May be it makes sense to ask
> upstream.
>  
> >   About 2), I should be able to package the new version. I just want
> > to be sure that nobody is currently doing it.
> 
> I'd be happy if you would do it.
>  
> Kind regards
> 
>        Andreas. 
> 
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> http://fam-tille.de
> 
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