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

[Hoyle, Alan P]

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.  Python is completely unrelated to samtools in my mind, except that it's a requirement for cwltool.

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.

That way I wouldn't need to include --no-install-recommends whenever I apt-get install samtools.

Thanks, alan


--
Alan Hoyle - alanh at unc.edu
Bioinformatics Scientist
UNC Lineberger - Bioinformatics Core
https://lbc.unc.edu/

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