Install SimpleElastix with Python3 on the O2 server at Harvard Medical School

install_SimpleElastix.sh

#!/bin/bash
#SBATCH --job-name=installSE
#SBATCH -c 4                # Number of cores
#SBATCH -t 0-03             # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p short            # Partition to submit to, whichever is faster
#SBATCH --mem-per-cpu=4G    # Memory (see also --mem)
#SBATCH -o joboutput.out    # job output
#SBATCH -e joberrors.err    # job error log

# load modules
module load gcc/6.2.0 python/3.7.4 cmake/3.14.1

# paths
export VENVPATH="/home/$(whoami)/se_venv"
export CODEPATH="/home/$(whoami)/SimpleElastix"

# create virtual environment
virtualenv $VENVPATH
source "$VENVPATH/bin/activate"

# download code for installation
git clone https://github.com/SuperElastix/SimpleElastix $CODEPATH

# configure installation
# check this link for background information
# https://github.com/rcasero/pysto/wiki/Build-and-install-SimpleElastix-for-python-3.x
mkdir "$CODEPATH/build"
cd "$CODEPATH/build"
cmake -DPYTHON_EXECUTABLE:FILEPATH="$VENVPATH/bin/python3" \
    -DPYTHON_LIBRARY:FILEPATH="$VENVPATH/lib/python3.7" \
    -DPYTHON_INCLUDE_DIR:PATH="$VENVPATH/include/python3.7m" \
    -DBUILD_EXAMPLES=OFF \
    -DBUILD_TESTING=OFF \
    "$CODEPATH/SuperBuild"

# install the main component
make -j4

# install the Python-related components
cd "$CODEPATH/build/SimpleITK-build/Wrapping/Python"
python "Packaging/setup.py" install

The O2 server hasn't supported Docker engine yet and the Python path issue took me quite some time, so here's the script that may save you some time

Thank you soo much!