Re: Debian package bcftools

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Giulio,

How would you like the idea to have both Perl and Python as recommended
and only leave the latex as suggested? What should then happen is that
we place this as a bug report against bcftools. The maintainer (should)
see(s) this and you will be informed when the upload happened that
implements your suggestion. I expect this to be associated with an
upcoming new upstream version, but, hey, we have the Covid-19 hackathon
this week, feel free have this as your first active contribution if
there are no ultimate negative vibes emerging on this list about a
demotion of the strict dependency on Perl. I happily talk you through.
To shorten bits up, I have just created the bug report -
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962834 .

Thank you tons for your feedback. Please keep it coming.

Steffen

On 14.06.20 20:35, Giulio Genovese wrote:
> Hi Steffen,
>
> Thank you for your reply. Yes, I am aware of the
> --no-install-recommends option but currently the bcftools package has
> the following dependencies:
> Depends: libc6 (>= 2.29), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), perl:any
> Suggests: python, python-numpy, python-matplotlib,
> texlive-latex-recommended
> So that the --no-install-recommends option works to avoid the python
> dependencies but not the perl dependencies. Notice that bcftools
> contains the following binaries:
> /usr/bin/bcftools <- C binary
> /usr/bin/color-chrs.pl <http://color-chrs.pl> <- to be used with
> bcftools +color-chrs plugin
> /usr/bin/guess-ploidy.py <- ro be used with bcftools +guess-ploidy plugin
> /usr/bin/plot-roh.py <- to be used with bcftools roh
> /usr/bin/plot-vcfstats <- to be used with bcftools stats
> /usr/bin/run-roh.pl <http://run-roh.pl> <- to be used with bcftools roh
> /usr/bin/vcfutils.pl <http://vcfutils.pl> <- standalone tool
> I suppose only the last one might be of interest but I confess I have
> never used it.
>
> I am also aware of being able to manually delete perl after having it
> installed as a dependency through installing bcftools. But since
> python is a suggested dependency, couldn't also perl be made as one? I
> am definitely not advocating for the perl (and python) binaries to be
> removed from the bcftools package, as they are very small anyway. Do
> you think there would be many users that would get the "perl not
> found" error when trying to run vcfutils.pl <http://vcfutils.pl> if
> perl is moved from a mandatory to a suggested dependency?
>
> Giulio
>
> On Sun, Jun 14, 2020 at 2:15 PM Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>> wrote:
>
>     Actually, I appreciate your forward to this mailing list - it is some
>     nice food for thought. We may yet have been mostly concerned about
>     maintainability, less so on specifying fractions of workflows that
>     complete workflows.
>
>     @Gulio, are you are of the --no-install-recommends option to apt-get
>     install? Would that allow you to circumvent your concern to optimise
>     your docker image? Also, you can possibly remove all the binaries you
>     don't need to reduce the final size of your image, right? Maybe
>     you want
>     to remove parts of packages after an installation, like in
>     dpkg -L bcftools | grep '^/usr/share/doc' | xargs -r rm ?
>
>     Olivier may have additional ideas.
>
>     Best,
>     Steffen