deepmrseg_singularity.def

Bootstrap: docker
From: tensorflow/tensorflow:2.3.3-gpu-jupyter

%help

	To install python libraries after this image is built, create a virtual environment that uses the system packages with `virtualenv --system-site-packages venv && source venv/bin/activate`, then use `pip` as usual.


%environment

%post
	NOW=`env TZ=America/New_York date`
	echo "export NOW=\"${NOW}\"" >> $SINGULARITY_ENVIRONMENT

%runscript
	echo "\n\nContainer was created: $NOW"
	echo "Python version: `python --version`"
	echo "Python exec: `which python`"
	echo "Arguments received: $*\n\n"
	exec "$@"


%post
	export DEBIAN_FRONTEND=noninteractive
	ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
	apt-get update
	apt-get -y install python3-tk --fix-missing
	
	# need to create mount point for home dir, scratch
	mkdir /uufs /scratch

	pip install --upgrade setuptools
%test
	# Sanity check that the container is operating

	# Test numpy 
	python -c "import numpy as np;np.__config__.show()"

	# Ensure that TensorFlow can be imported and session started (session start touches GPU)
	python -c "import tensorflow as tf;s = tf.constant( 1.0, tf.float32 )"



###############################
### DEEPMRSEG
###############################

%environment        

%post
        echo "\n\n Installing DeepMRSeg \n\n"

	mkdir -p /opt/cbica/src/deepmrseg \
	&& cd /opt/cbica/src/deepmrseg \
	&& git clone https://github.com/CBICA/DeepMRSeg.git \
	&& cd DeepMRSeg \
	&& python setup.py install \
	&& rm -rf /opt/cbica/src/deepmrseg \
	&& rmdir /opt/cbica/src /opt/cbica

%test
        echo "\nTesting DeepMRSeg exec(s)"
        which deepmrseg_train
	deepmrseg_train