runScript.sh

#!/bin/bash
#SBATCH --job-name py_run           # Job name
#SBATCH -p a100_normal_q                # partition name
#SBATCH -t 0-4:00               # hours:minutes runlimit after which job will be killed
#SBATCH --nodes=4            # number of cores requested -- this needs to be greater than or equal to the number of cores you plan to use to run your job
#SBATCH --mem-per-cpu=8G
#SBATCH --account=rnaseq-pilotlab


module load site/tinkercliffs-rome/easybuild/setup
module load site/tinkercliffs/easybuild/setup
module load Biopython/1.78-foss-2020b

import pandas as pd
read_file = pd.read_csv (r'/projects/rnaseq-pilotlab/icm/reports/featurecounts')
mkdir -p /projects/rnaseq-pilotlab/icm/reports/cvs_file

read_file.to_csv (r'/projects/rnaseq-pilotlab/icm/reports/cvs_file/'*.txt.csv, index=None)
#export CONDA_ENV=__init__.py
#source activate __init__.py
#conda install -c conda-forge biopython
#conda install jupyter
#conda install pandas
#jupyter notebook --config=/config.py