Re: package bcftools dependencies for gff2gff.py and guess-ploidy.py cause bcftools to have 10x as many dependencies

My use case is docker images. I basically cannot use the bcftools debian
package anymore to build containers as it balloons the size of the final
image. Appreciate forwarding to the Debian Med team. Thank you. -Giulio

On Tue, Jun 18, 2024 at 3:03 PM Andreas Tille <[email protected]> wrote:

> Hi Giulio,
>
> I'm forwarding this to the Debian Med team since as DPL I have basically
> stalled my packaging work.
>
> My gut feeling tells me that 500MB are not really much on a
> bioinformatitions machine - specifically since python3-matplotlib seems
> to be nearly a "default installation" on scientists computers.  But well,
> maybe Recommends are fine and possibly some Test-Depends need to be
> added (not checked!)
>
> Kind regards
>     Andreas.
>
> Am Tue, Jun 18, 2024 at 02:37:48PM -0400 schrieb Giulio Genovese:
> > Hi Andreas,
> >
> > To address bug #1069234
> > <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1069234> the bcftools
> > package acquired, through commit a46c2e25
> > <
> https://salsa.debian.org/med-team/bcftools/-/commit/a46c2e2567ffcbac0099f102c6bcac2568f100a8
> >,
> > two new dependencies:
> > - python3-gffutils
> > - python3-matplotlib
> > This causes the size of the package dependencies to explode from <50MB to
> > >500MB.
> >
> > As bcftools is mostly a C software, I believe the most appropriate
> approach
> > is to have those dependencies as recommended dependencies, so that the
> > package can be installed in a minimalistic fashion with the apt-get
> > --no-install-recommends command while not affecting other use cases,
> > similarly to how it was done for the bwa package in commit e3fef43e
> > <
> https://salsa.debian.org/med-team/bwa/-/commit/e3fef43e17a26dd0c1c7d7ac81333a0e9c6367b3
> >
> > where perl was demoted to a recommended dependency.
> >
> > I hope this change can be included for the next release. Thank you!
> >
> > Giulio
>
> --
> https://fam-tille.de
>