Samtools not installing properly on mac

Question

[Sarah]

Hi there,

I have been struggling quite a bit with using UMItools lately and deduplicating my files. I think this may be due to samtools not being installed correctly/ not having the correct version installed. This is because some commands I try to use (from https://genomics.sschmeier.com/ngs-mapping/index.html?highlight=samtools#before-we-start) return an error code saying command not recognised ie

[main] unrecognized command 'markdup'

or samtools: invalid option – m

I have tried updating to the new version but this is not working out for me. Basically, I had first installed samtools using homebrew:

$ brew install samtools

When I type samtools into my command line, it shows me that the version I have installed is 1.19.2 and the markdup command does not show up as one of the commands listed in the response generated.

Next, I tried to install the latest version using the following command:

conda install -c bioconda samtools 

Now when I type samtools into the command line, I get this error code:

dyld[37839]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: <8AD915FB-8A79-34FD-9167-D77089463421> /Users/malh763/miniconda3/bin/samtools
  Reason: tried: '/Users/malh763/miniconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/Users/malh763/miniconda3/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file, not in dyld cache)
zsh: abort      samtools

Then I try to install it again using home brew and when I type samtools into the command line it gives me the same error as above and now the lines of UMItools code that used to work before no longer work for me. What do I do?

[ATpoint]

Be sure that your .condarc file lists the channels in correct order:

channels:
  - conda-forge
  - bioconda
  - defaults

...or use mamba rather than conda which in my experience is better at solving dependencies out of the box.