Installing samtools version 1.12

Question

[irfanwustl]

I am trying to install samtools version 1.12 in a new conda environment. The command I am using:

conda install -c bioconda samtools=1.12

However, it seems there are some conflicts.

I can easily install other versions like 1.11 but not this one. (I need this version as -N option is added to the samtools view in this version). I have found this but does not say how to install it with conda.

Answer 1

[Devon Ryan]

Make sure to specify conda-forge as well:

conda install -c conda-forge -c bioconda samtools=1.12

If there are still conflicts, then they're with something in your current environment. In that case make a new environment:

conda create -n samtools112 -c conda-forge -c bioconda samtools=1.12

[irfanwustl]

Thank you so much. It works.

[jkbonfield]

Isn't this just overly tight requirements in Conda? I'm not aware of samtools very precisely needing ncurses between versions 6.2 and 6.3.0a0. Adding arbitrary limits to packages like this causes problems, and just asking for a new environment is simply a workaround. It's hardly fixing the route cause of the problem.

Again zlib version makes no sense here. We don't have specific zlib versions we require. (Also you're far better off using libdeflate, although it may still also need zlib for something. I forget now if we can get away without zlib at all.)

Finally, I'd recommend people try Mamba instead as it sometimes solves these resolver issues, plus it's lightningly fast compared to conda's resolver.

[Devon Ryan]

The pinnings could well be a bit restrictive, we'd have to take that up with conda-forge, since they're coordinated across all packages in both projects.