Clone the repository with submodules:
git clone --recursive https://github.com/JaneliaSciComp/expansion-microscopy-pipeline.git
If you have already cloned the repository, run this after cloning to fetch the submodules:
git submodule update --init --recursive
To update the external modules:
git pull --recurse-submodules
To make changes to a submodule, cd into its directory and then checkout the master branch:
cd external-modules/spark
git checkout master
Commit as normal, then back at the root update the submodule commit pointer and check it in:
git submodule update --remote
git commit external-modules/spark -m "Updated submodule to HEAD"
All containers used by the pipeline have been made available on Docker Hub. You can rebuild these to make customizations or to replace the algorithms used. To build the containers and push to Docker Hub you can install maru and run maru build.
To push to Docker Hub, you need to login first:
docker login
To push to AWS ECR, you need to login as follows:
aws ecr-public get-login-password --region us-east-1 | docker login --username AWS --password-stdin public.ecr.aws