[Debian-med-packaging] Samtools rec: dependencies are too aggressive.

[Hoyle, Alan P]

I have submitted a bug report referencing the issue and your git updates.

Bug#963093: samtools: recommended dependencies are unnecessary

Thank you Andreas!
________________________________
From: Andreas Tille <andreas at an3as.eu>
Sent: Thursday, June 18, 2020 3:34 PM
To: Hoyle, Alan P <alanh at email.unc.edu>
Cc: samtools at packages.debian.org <samtools at packages.debian.org>
Subject: Re: Samtools rec: dependencies are too aggressive.

Hi Alan,

On Thu, Jun 18, 2020 at 04:06:09PM +0000, Hoyle, Alan P wrote:
> There's no particular hurry to fix things from my perspective: my use case is relatively obscure, with an easy work-around (--no-install-recommends), and even if I forget the only costs are slightly bigger images and slightly slower installs.

Bug that was proxy-files by Steffen is fixed now (hopefully).

> This was my first time making a suggestion about a debian package, so I tried the method documented at https://www.debian.org/contact

Well

   https://www.debian.org/contact#packageproblems

gives "instructions for filing bug reports" which presents
as first sentence

  We strongly recommend that you report bugs in Debian using the reportbug program.

;-)

> It didn't seem like this was a "bug" the way I thought about it:  I mean, everything does actually work, it just installs extra stuff, so I thought I would do the second method listed there and email the maintainer directly.

This is definitely a bug for you - of severity wishlist or minor
depending how you feel about it.

> At this point, would it be helpful if I created a bug report for this issue?

As I wrote below I've fixed in Git.  If you want this properly documeted
its possible even now OK to use reportbug.  But may be we do not need this
post-fixed-situation bureaucracy.  Just tell me whether you want me to
upload the package soonish.

> Note that my primary use of debian is through container images (Docker and Singularity) , so I'd have to make a special image to install reportbug.

In any case it would be sensible to have one instance featuring reportbug
for this purpose.

Kind regards

      Andreas.

> -alan
>
>
> ________________________________
> From: Andreas Tille <andreas at fam-tille.de>
> Sent: Tuesday, June 9, 2020 5:41 AM
> To: Hoyle, Alan P <alanh at email.unc.edu>
> Cc: samtools at packages.debian.org <samtools at packages.debian.org>
> Subject: Re: Samtools rec: dependencies are too aggressive.
>
> Hi Alan,
>
> thank you for your comments on samtools packaging.  In general it would
> be prefered if you fire up reportbug to report issues like this since
> the issue is documented in an easily accessible way and we can properly
> close the issue.
>
> On Mon, Jun 08, 2020 at 10:42:09PM +0000, Hoyle, Alan P wrote:
> > I have been using samtools for many HTS workflows now, and I recently started building some Docker images that need to include it.
> >
> > I noticed that apt-cache depends samtools lists as "Recommends" packages both cwltool and python.
> >
> > I suggest that if someone knows they need cwltool (I've used it), they will install it separately.  I can see samtools as Recommends for cwltool given the frequency that HTS workflows would need it.
>
> That's fixed in packaging git now:
>
>     https://salsa.debian.org/med-team/samtools/-/commit/e8c62ffa10f390937a225fb4188fa9c31510379a
>
> (If there would be a bug report I would tag it as "pending upload")
>
> > Python is completely unrelated to samtools in my mind, except that it's a requirement for cwltool.
>
> ACK.  That dependency was added 10 years ago.  Currently I can also not
> find any Python dependency and thus I commited
>
>     https://salsa.debian.org/med-team/samtools/-/commit/81ac71e9ddacb88279c35a913c81ba8f5118720a
>
> > If anything, I think that those cwltool dependency can be changed from "Recommends" to "Suggests", and I think the python dependency could be removed entirely, given that cwltool already has python3 as a dependency.
>
> I fully agree.  Thanks a lot for your comments.
>
> > That way I wouldn't need to include --no-install-recommends whenever I apt-get install samtools.
>
> Let me know if you want us to upload soon to help you immediately.
>
> Kind regards
>
>        Andreas.
>
> --
> http://fam-tille.de

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