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Andreas,</div>
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Thank you for your attention on this. Your email ended up in my spam folder, so I just saw it this morning. </div>
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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. </div>
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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></div>
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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. </div>
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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. </div>
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-alan</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Andreas Tille <andreas@fam-tille.de><br>
<b>Sent:</b> Tuesday, June 9, 2020 5:41 AM<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>
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<div class="PlainText">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>
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