Re: hts-nim-tools ready for peer review
On 07.11.20 23:11, Nilesh Patra wrote:
> Hi
>
> On Sun, 8 Nov 2020 at 01:41, Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>> wrote:
>
> https://salsa.debian.org/med-team/hts-nim-tools
> <https://salsa.debian.org/med-team/hts-nim-tools>
>
> Hello,
>
> It is one fat binary that acts as both a container and a wrapper
> of all
> the other executables. This should help avoid name conflicts and
> we can
> still patch bcbio should this turn out to be required. It is also how
> upstream wants it to be compiled, so we should be fine.
>
>
> Great!
> I did a few changes which I would call as rather nitpicky changes -
> The package looked more or less, perfect to me before I did so as well.
> NB: I added in an autopkgtests but this is not exhaustive since this
> does not test all the binaries provided by the package, I could not
> find suitable data to test "count-reads" and "vcf-check" probably due
> to my lack of knowledge in bioinformatics or medical science in general.
> Please consider to enhance tests if you'd know the data this might
> work on to be added as tests.
Thank you!
We should work with upstream on the testing. When upstream knows that
what is in Debian is treated (and tested) in a way they are happy with
then there is no reason not to endorse our packages.
>
>
> This is a top-level package from bcbio's point of view, i.e.
> please take
> your time. I'll address nim-d3 next and the reupload of seqcluster.
> There there is pyomo and then ... donno, I expect we get fairly far at
> least with a subset of the bcbio workflows that do not use snpeff such
> that bcbio can transition to testing.
>
>
> Thanks a lot for packaging this HUGE chain of dependencies! :-)
Well. That is a team effort, as you keep proving.
Best,
Steffen
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