initializing conda

[nick-youngblut]

None of the profiles seem to include an initialization of conda, such as . ~.bashrc in which with the .bashrc includes the standard setup:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/ebio/abt3_projects/software/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/ebio/abt3_projects/software/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/ebio/abt3_projects/software/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/ebio/abt3_projects/software/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

How does one use conda with any of the snakemake profiles? I've always used the following for my sge profile job script template:

#!/bin/bash
export OMP_NUM_THREADS=1
# properties = {properties}
 . ~/.bashrc
{exec_job}

... but since snakemake>5.25 I've been getting Perl and Python sys path issues (snakemake/snakemake#786). I was wondering if this is due to my job script (eg., may initializing conda isn't needed?). However, if I remove . ~/.bashrc from my job template script, all of the qsub jobs submitted by snakemake die and do not produce a log file. The sge stdout file is empty and the stderr file just contains the standard info, for example:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 128
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	validate_read2
	1
Select jobs to execute...
WorkflowError:
Failed to solve the job scheduling problem with pulp. Please report a bug and use --scheduler greedy as a workaround:
Pulp: Error while trying to execute, use msg=True for more detailscbc

I'm currently running snakemake 5.30.1. The cluster is running Ubuntu 18.04.5