README.md

Pipeline for cell registration across multiple sessions

Environment configuration

This package is intended for use on Oscar with GPU support for PyTorch.

To use on Oscar, first clone the repo. Then load the anaconda module:

module load anaconda/2022.05
source /gpfs/runtime/opt/anaconda/2022.05/etc/profile.d/conda.sh

If you have never loaded the anaconda/2022.05 module before, you need to initialize the conda module by running the following command.

conda init bash

For more information on working with conda on Oscar, please consult this page.

Once the anaconda module is loaded, please create a new environment using the environment.yml file:

conda env create -n cellreg -f environment.yml

where cellreg is the name of your environment. Please be patient as conda is slow on Oscar. Once the environment has been created, activate the environment with

conda activate cellreg