Great Lakes

Setup on a desktop

module load singularity
# now change to a directory with enough storage, e.g. /nfs/turbo/username
git clone https://github.com/neurodesk/neurocommand.git
cd neurocommand
pip3 install -r neurodesk/requirements.txt --user
bash build.sh --cli
bash containers.sh
export SINGULARITY_BINDPATH=`pwd -P`
bash containers.sh itksnap
# now select a version of itksnap to install. For this copy and paste the installation
echo "module load singularity" >> ~/.bashrc
echo "module use $PWD/local/containers/modules/" >> ~/.bashrc
echo "export SINGULARITY_BINDPATH=/nfs/,/scratch/" >> ~/.bashrc

Setup with a jupyter notebook

Start a new Jupyter notebook by entering “load singularity” in the Module Commands field:

Then run these commands:

!pip install jupyterlmod

# Restart the kernel by clicking Kernel -> Restart Kernel

import module
await module.load('niimath')