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 <- 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 <- to be used with bcftools roh
/usr/bin/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 if perl is moved from a mandatory to a suggested dependency?
Giulio
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