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

[Hoyle, Alan P]

Andreas,

Thank you for your attention on this.  Your email ended up in my spam folder, so I just saw it this morning.

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.

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

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.

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

-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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200618/791312ee/attachment-0001.html>