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.
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! :-)
Kind Regards,
Nilesh