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

[Andreas Tille <andreas@an3as.eu>]

Hi again,

Am Tue, Jun 18, 2024 at 04:04:21PM -0400 schrieb Giulio Genovese:
> 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

Sounds sensible.  Would you mind summarising all the reasons you gave in
some bug report (`reporbug bcftools`) to make sure it does not get
forgotten?

Thank you
   Andreas.

> On Tue, Jun 18, 2024 at 3:03 PM Andreas Tille <andreas@an3as.eu> 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
> >

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