datalad_run.bash

### datalad container version

# add the container to datalad
CONTAINER_VERSION=20.2.1lts
datalad containers-add --url docker://poldracklab/fmriprep:${CONTAINER_VERSION} -i ./derivatives/fmriprep fmriprep-${CONTAINER_VERSION}

PROJECT_PATH="/lustre03/project/6003287"
DATASET_PATH=$1
DATASET_FOLDER="${DATASET_PATH%/*}"
PYTHON_CMD="python /fmriprep-slurm/fmriprep-slurm/main.py "$@

echo "Running fmriprep-slurm "$@
export SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow
module load singularity/3.6

echo $PYTHON_CMD | xargs singularity exec -B $PROJECT_PATH/fmriprep-slurm:/fmriprep-slurm \
  -B $DATASET_FOLDER:/DATA -B /etc/pki:/etc/pki \
  -B /home/$USER/.cache/templateflow:/templateflow \
  $PROJECT_PATH/derivatives/fmriprep/fmriprep-${CONTAINER_VERSION}

# now you can use it
datalad containers-run --name fmriprep-${CONTAINER_VERSION}

### datalad run version
datalad run ${PROJECT_PATH}/fmriprep-slurm/singularity_run.bash $@