main

#!/bin/bash
#PBS -k o
#PBS -l nodes=1:ppn=16,walltime=12:00:00

## modules
echo "Loading modules"
module load ants
module unload matlab
module load matlab/2017a
module load spm/8
module unload python
module load dipy/dev
module load nodejs
module unload mrtrix/0.2.12 
module load mrtrix/0.3.15
module unload fsl
module load fsl/5.0.9
module unload freesurfer/5.3.0
module load freesurfer/6.0.0
echo "Finished loading modules"

export PYTHONPATH=/N/u/brlife/git/nibabel:$PYTHONPATH

#execute app
./run.sh

ret=$?
if [ ! $ret -eq 0 ]; then
	exit $ret
fi

#removing files
rm *.trk -f
rm *.tck -f
rm *.nii.gz -f
rm -r tractograms_directory -f
rm -r examples_directory* -f
rm kdt -f
rm prototypes.npy -f
rm -r aligned_ROIs -f
rm -r templates -f
rm distance* -f

echo "Complete"