#!/bin/bash
#SBATCH --job-name=pySCENIC-0.12.1-case
#SBATCH --partition=batch
#SBATCH --time=05:00

# conda commands
module load gcc/10.2.0 miniconda3
source $CONDA_PROFILE/conda.sh
conda activate /mnt/apps/prebuilt/pySCENIC/env
export PATH=$CONDA_PREFIX/bin:$PATH

# CLI use (standalone): Run pySCENIC commands from Terminal
pyscenic -h
# pyscenic grn <expression_mtx_fname> <tfs_fname> -ο <OUTPUT> --num_workers $PBS_NTASKS
# etc etc ...

# Use as python library: See example script run below
python pySCENIC_code.py