<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I have submitted a bug report referencing the issue and your git updates. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Bug#963093: samtools: recommended dependencies are unnecessary<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Thank you Andreas! </div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Andreas Tille <andreas@an3as.eu><br>
<b>Sent:</b> Thursday, June 18, 2020 3:34 PM<br>
<b>To:</b> Hoyle, Alan P <alanh@email.unc.edu><br>
<b>Cc:</b> samtools@packages.debian.org <samtools@packages.debian.org><br>
<b>Subject:</b> Re: Samtools rec: dependencies are too aggressive.</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi Alan,<br>
<br>
On Thu, Jun 18, 2020 at 04:06:09PM +0000, Hoyle, Alan P wrote:<br>
> 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.<br>
<br>
Bug that was proxy-files by Steffen is fixed now (hopefully).<br>
<br>
> This was my first time making a suggestion about a debian package, so I tried the method documented at
<a href="https://www.debian.org/contact">https://www.debian.org/contact</a><br>
<br>
Well<br>
<br>
<a href="https://www.debian.org/contact#packageproblems">https://www.debian.org/contact#packageproblems</a><br>
<br>
gives "instructions for filing bug reports" which presents<br>
as first sentence<br>
<br>
We strongly recommend that you report bugs in Debian using the reportbug program.<br>
<br>
;-)<br>
<br>
> 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.<br>
<br>
This is definitely a bug for you - of severity wishlist or minor<br>
depending how you feel about it.<br>
<br>
> At this point, would it be helpful if I created a bug report for this issue?<br>
<br>
As I wrote below I've fixed in Git. If you want this properly documeted<br>
its possible even now OK to use reportbug. But may be we do not need this<br>
post-fixed-situation bureaucracy. Just tell me whether you want me to<br>
upload the package soonish.<br>
<br>
> 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.<br>
<br>
In any case it would be sensible to have one instance featuring reportbug<br>
for this purpose.<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
> -alan<br>
> <br>
> <br>
> ________________________________<br>
> From: Andreas Tille <andreas@fam-tille.de><br>
> Sent: Tuesday, June 9, 2020 5:41 AM<br>
> To: Hoyle, Alan P <alanh@email.unc.edu><br>
> Cc: samtools@packages.debian.org <samtools@packages.debian.org><br>
> Subject: Re: Samtools rec: dependencies are too aggressive.<br>
> <br>
> Hi Alan,<br>
> <br>
> thank you for your comments on samtools packaging. In general it would<br>
> be prefered if you fire up reportbug to report issues like this since<br>
> the issue is documented in an easily accessible way and we can properly<br>
> close the issue.<br>
> <br>
> On Mon, Jun 08, 2020 at 10:42:09PM +0000, Hoyle, Alan P wrote:<br>
> > I have been using samtools for many HTS workflows now, and I recently started building some Docker images that need to include it.<br>
> ><br>
> > I noticed that apt-cache depends samtools lists as "Recommends" packages both cwltool and python.<br>
> ><br>
> > 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.<br>
> <br>
> That's fixed in packaging git now:<br>
> <br>
> <a href="https://salsa.debian.org/med-team/samtools/-/commit/e8c62ffa10f390937a225fb4188fa9c31510379a">
https://salsa.debian.org/med-team/samtools/-/commit/e8c62ffa10f390937a225fb4188fa9c31510379a</a><br>
> <br>
> (If there would be a bug report I would tag it as "pending upload")<br>
> <br>
> > Python is completely unrelated to samtools in my mind, except that it's a requirement for cwltool.<br>
> <br>
> ACK. That dependency was added 10 years ago. Currently I can also not<br>
> find any Python dependency and thus I commited<br>
> <br>
> <a href="https://salsa.debian.org/med-team/samtools/-/commit/81ac71e9ddacb88279c35a913c81ba8f5118720a">
https://salsa.debian.org/med-team/samtools/-/commit/81ac71e9ddacb88279c35a913c81ba8f5118720a</a><br>
> <br>
> > 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.<br>
> <br>
> I fully agree. Thanks a lot for your comments.<br>
> <br>
> > That way I wouldn't need to include --no-install-recommends whenever I apt-get install samtools.<br>
> <br>
> Let me know if you want us to upload soon to help you immediately.<br>
> <br>
> Kind regards<br>
> <br>
> Andreas.<br>
> <br>
> --<br>
> <a href="http://fam-tille.de">http://fam-tille.de</a><br>
<br>
> _______________________________________________<br>
> Debian-med-packaging mailing list<br>
> Debian-med-packaging@alioth-lists.debian.net<br>
> <a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging">
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging</a><br>
<br>
<br>
-- <br>
<a href="http://fam-tille.de">http://fam-tille.de</a><br>
</div>
</span></font></div>
</body>
</html>