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

[Andreas Tille]

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. :-)

> 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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