sbatch_step2.sh

#!/bin/bash
##### Job definition
#SBATCH --nodes=1					# OpenMP requires a single node
#SBATCH --ntasks=1					# Run a single serial task
#SBATCH --time=00:10:00				# Time limit hh:mm:ss
#SBATCH -e step2_error_%A_%a.log			# Standard error
#SBATCH -o step2_output_%A_%a.log			# Standard output
#SBATCH --job-name=bidstrain			# Descriptive job name
#SBATCH --partition=serial

##### load required modules

module load singularity

##### run container commands

# training on the sample data
singularity run --bind /scratch/psyc5171/amw17004/bidscoiner:/data \
	/scratch/psyc5171/containers/birc-bids_latest.sif \
	bidstrainer.py /data/bids


# Create the bidsmap
singularity run --bind /scratch/psyc5171/amw17004/hw2:/data \
	/scratch/psyc5171/containers/birc-bids_latest.sif \
	bidsmapper.py -t /data/bids/code/bidscoin/bidsmap_sample.yaml \
	-i 0 /data/raw  /data/bids