On 07.11.20 23:11, Nilesh Patra wrote: > Hi > > On Sun, 8 Nov 2020 at 01:41, Steffen Möller <[email protected] > <mailto:[email protected]>> 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
