Using profile without using --conda-not-block-search-path-envvars

[nick-youngblut]

At least for snakemake 5.32, I can't use my snakemake SGE profile without using the new parameter --conda-not-block-search-path-envvars. If I don't provide the parameter, I get an import error when snakemake calls my job submission script:

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'

The top of my job submission script:

#!/usr/bin/env python3
import os
import sys
import re
import subprocess

from snakemake.utils import read_job_properties

My sge-jobscript.sh:

#!/bin/bash
export OMP_NUM_THREADS=1
# properties = {properties}
if [[ -f ~/.bashrc &&  $(grep -c "__conda_setup=" ~/.bashrc) -gt 0 && $(grep -c "unset __conda_setup" ~/.bashrc) -gt 0 ]]; then
   echo "Sourcing .bashrc" 1>&2
   . ~/.bashrc
else
   echo "Exporting conda PATH" 1>&2
   export PATH=/ebio/abt3_projects/software/dev/miniconda3_dev/bin:$PATH
fi

How do I avoid having to use --conda-not-block-search-path-envvars every time I run snakemake? I tried adding conda activate snakemake to the bottom of my sge-jobscript.sh, but that didn't help