jlanga
commented
2 months ago Hi @Adam-Staniszewski.
The module that you use to load snakemake doesn't come with pandas. It must be way too old. Snakemake has been forcing the installation of pandas for a while. It is one of many mandatory dependencies. In conda it is installed out of the box: https://bioconda.github.io/recipes/snakemake/README.html
Make sure that you are using snakemake 8, and if you are using modules, that the other dependencies are there too.
Kind regards,
Jorge
Hi,
I went through all the past issue and hit the same problems as previous users.
/smsk_popoolation$ snakemake --conda-create-envs-only Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.
When I go with certain number of cpus or --cores all always get following error:
ModuleNotFoundError in line 3 of /home/*/smsk_popoolation/workflow/Snakefile: No module named 'pandas'
I tried to work it around by installing pandas in the env or adding pandas to dependencies in smsk_popoolation/workflow/rules/helpers/environment.yml, nothing changed, same error with pandas occurs
Could you update documentation to workable version ?
Thank you