I just updated from snakemake 5.28 to 5.32, and now from snakemake.utils import read_job_properties throws an import error for my job submission script in my snakemake profile:
Traceback (most recent call last):
File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgqc/bin/ll_pipeline_utils/profiles/sge/sge-submit.py", line 7, in <module>
from snakemake.utils import read_job_properties
ModuleNotFoundError: No module named 'snakemake'
Using --conda-not-block-search-path-envvars prevents this import error, but I'd rather not have to use --conda-not-block-search-path-envvars every time I run snakemake.
I don't see anything special that the SLURM snakemake profile uses to get around this import issue, so I really don't know what to do besides using --conda-not-block-search-path-envvars all of the time.