Re: Debian package bcftools

[Steffen Möller]

Excellent, please
 * get an account on salsa.debian.org and request membership with the
med-team
 * find a tutorial on how git works, not to know everything but so you
can distinguish branches from tags
 * have a Debian machine (or a cloud/docker instance) with Debian
unstable so you can install build dependencies and test your package
 * find a time to sync up with on one of the upcoming evenings for a
live session - we are both on central European summer time? The process is
    - install git-buildpackage
    - gbp clone --pristine-tar https://salsa.debian.org/med-team/bcftools
    - do the right set of changes, commit them locally
    - gbp buildpackage
    - test, push changes back to salsa
    - request sponsoring

    For any questions that arise in between just send me an email and I
answer as soon as I can.

 * have a peek at
https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?usp=sharing
and to see if there is a software close to your heart that you would
want to see prepared for the distribution - feel free to add something

Best,

Steffen


On 15.06.20 01:01, Giulio Genovese wrote:

Hi Steffen,

Yes, that would be great. I didn't even know there was a three tier of
mandatory/recommended/suggested packages, or I would have suggested
the same solution you proposed to begin with. I am a bit new to this
so I would be happy to help in the way I can if you want to talk me
through it. Feel also free to write to me on my personal email account.

Giulio

On Sun, Jun 14, 2020 at 6:51 PM Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:

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

Re: Debian package bcftools

[Giulio Genovese]

Hi Steffen,

Yes, that would be great. I didn't even know there was a three tier of
mandatory/recommended/suggested packages, or I would have suggested the
same solution you proposed to begin with. I am a bit new to this so I would
be happy to help in the way I can if you want to talk me through it. Feel
also free to write to me on my personal email account.

Giulio

On Sun, Jun 14, 2020 at 6:51 PM Steffen Möller 
wrote:

> 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
>

Re: Debian package bcftools

[Steffen Möller]

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  <- 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

On Sun, Jun 14, 2020 at 2:15 PM Steffen Möller mailto:steffen_moel...@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

Re: Debian package bcftools

[Giulio Genovese]

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

On Sun, Jun 14, 2020 at 2:15 PM Steffen Möller 
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
>

Re: Debian package bcftools

[Steffen Möller]

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

On 13.06.20 21:10, Michael Crusoe wrote:

[I'm cc'ing the Debian Med mailing list as your email contains no
private information]

Dear Giulio,

It is nice to hear that you are finding the Debian package of bcftools
useful. The correct way to request support from the volunteer
contributors to Debian is to documented at
https://www.debian.org/Bugs/Reporting


Cheers!

--
Michael R. Crusoe

On Sat, Jun 13, 2020, 20:0 Giulio Genovese mailto:giulio.genov...@gmail.com>> wrote:

Hi Michael,

I have noticed you are involved in the packaging of the bcftools
software as a debian package. I am not sure whether you are the
right person I should address, but if not maybe you can help me
find who I should address instead.

I have been working with bcftools and in particular with dockers
that must run bcftools inside. This is all made very simple by the
bcftools debian package. However, I have noticed that the approach
of installing bcftools as a debian package causes apt-get to also
pull perl and perl modules which cause the docker image to
increase in size significantly. The bcftools package contains a
handful of python and perl binaries, but the main software is
written in C and has very few dependencies. Currently python is a
suggested dependency, while perl is a mandatory dependency. This
seems a bit inconsistent. Could the perl dependency also be made
optional? This would go a long way making it easier to generate
minimalistic docker images with a minimal footprint using apt-get.

All the best,

Giulio

Re: Debian package bcftools

[Michael Crusoe]

[I'm cc'ing the Debian Med mailing list as your email contains no private
information]

Dear Giulio,

It is nice to hear that you are finding the Debian package of bcftools
useful. The correct way to request support from the volunteer contributors
to Debian is to documented at https://www.debian.org/Bugs/Reporting

Cheers!

--
Michael R. Crusoe

On Sat, Jun 13, 2020, 20:0 Giulio Genovese 
wrote:

> Hi Michael,
>
> I have noticed you are involved in the packaging of the bcftools software
> as a debian package. I am not sure whether you are the right person I
> should address, but if not maybe you can help me find who I should address
> instead.
>
> I have been working with bcftools and in particular with dockers that must
> run bcftools inside. This is all made very simple by the bcftools debian
> package. However, I have noticed that the approach of installing bcftools
> as a debian package causes apt-get to also pull perl and perl modules which
> cause the docker image to increase in size significantly. The bcftools
> package contains a handful of python and perl binaries, but the main
> software is written in C and has very few dependencies. Currently python is
> a suggested dependency, while perl is a mandatory dependency. This seems a
> bit inconsistent. Could the perl dependency also be made optional? This
> would go a long way making it easier to generate minimalistic docker images
> with a minimal footprint using apt-get.
>
> All the best,
>
> Giulio
>