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

Vincent Danjean vdanjean.ml at free.fr
Sun Nov 6 10:56:28 UTC 2016


  Hi,

  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)
2) the htsjdk source package is still at 2.6.1+dfsg-1 in the archive
   (upstream released the 2.7.0 version)

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]).

  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)"
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.

  About 2), I should be able to package the new version. I just want
to be sure that nobody is currently doing it.

  Regards,
    Vincent

[1] https://github.com/broadinstitute/picard/issues/684

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