Re: picard-tools updated, and ready?
On 05/04/2018 02:30 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Fri, May 04, 2018 at 09:22:11AM +0200, Olivier Sallou wrote:
>> I have updated git repo for picard-tools.
>>
>> Dependencies are in java team (gkl, gatk-native-bindings, barclay) but
>> not uploaded yet. Instead I uploaded them to experimental for the
>> moment, waiting for full validation with picard-tools.
> Cool! From the naming it smells like a good precondition for GATK4
> which should be also packaged (rather sooner than later if I understood
> correctly).
>
>> I disabled unit tests due to a testng issue (I created a bug for this),
>> but I patched testng locally and could run all picard-tools unit tests.
> Sounds promising. Again, thanks a lot.
>
>> I think however that it would be nice to get other people validation for
>> picard-tools, if you could test build/run. Task was indeed not easy and
>> I'd like to be sure it works in other environments.
> I admit my hope to get more testers from this list is limited. (I
> explicitly added Vincent who is also in Uploaders but as far as I
> remember is not reading this list very regularly.) Thus I'd be in
> favour of uploading at least those preconditions to unstable. Since no
> package in unstable depends from these we can not really break anything.
> In general I also think that uploading to unstable even for picard-tools
> is fine (may be after testng bug is fixed) and use normal Debian QA
> tools as well as rdepends as "testers" in addition to potential readers
> here. We are in the middle of a release cycle and there is sufficient
> time to fix issues now.
>
>> I faced issues with Java 9 but more with Java 10 which is now default
>> (in fact may work only with Java 10+).
> Ahhh, will we see another Java migration before buster will be frozen?
>
>> I tested it with htsjdk from experimental.
> I guess there is no other chance since it depends from the version
> there, right?
I can't upload to unstable as one of the deps (gkl) depends on htsjdk ,
and need a *recent* one (the one in experimental works, the one in sid
fails).
So to upload those picard-tools deps, we first need to put htsjdk in sid
>
>> When I have green flag, I can upload new dependencies to unstable before
>> uploading picard-tools.
> So green flag from my side without testing anything since I do not even
> have a better idea how to test ...
>
> Kind regards
>
> Andreas.
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
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