jbloom/prjna692319_public

Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2

prjna692319_public's Issues

Making a new conda environment with environment.yml results in many conflicts

I'm not 100% sure I'm doing this right (the README could be more explicit), but when I make a new conda environment using the standard conda env create -f environment.yml I get a warning that conflicts are detected, followed some time later by thousands of lines of conda's obscure dump of conflicting package requirements.

I tried removing all the version specifiers (except Python 3.9) and got the same result. I then made a new environment without using the environment.yml and started installing packages to it, according to my rough guess at importance. When I got to snakemake conda said there was a conflict and gave the thousands of lines of output again...

In the end I just did stuff manually in my own way, running some of the commands manually (no snakemake), which of course has some benefit too (I also have alignments with bowtie2 and bwa).