Hi, I am trying to use mmseqs
as part of my nextstrain pipeline. I make added a rule in the Snakefile
that uses mmseqs directly but when running nextstrain build
I get:
/Users/vlad/.nextstrain/runtimes/conda/env/bin/bash: line 2: mmseqs: command not found
So while I have it installed on my machine it is not installed in the conda environment that nextstrain uses. Is there a way to install it in nextstrain? I am not sure how to manage its conda enviroment properly. My hacky shortcut was creating a symbolic link to the binary in the ~/.nextstrain/runtimes/conda/env/bin
but that is not portable.