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

Thank you soo much!