CGAP Pipeline Contribution

This repository contains modules contribued to CGAP pipelines through external collaborations.

Documentation

Documentation for the standard CGAP pipelines can be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/.

Initialize the Repository

Clone the repository. The submodules will be empty and set to the current commits saved for the main branch.

    git clone https://github.com/dbmi-bgm/cgap-pipeline-contribution.git

Check out the desired version. This will set the submodules to the commits linked for that specific release.

    git checkout <version>

Download the content for each submodule. The submodules will be set in detached state.

    make pull

Deployment Requirements

In order to deploy the pipelines pipeline_utils need to be installed and available in the environment. Please refer to the corresponding documentation here: https://portal-pipeline-utils.readthedocs.io/en/latest/.

The software can also be automatically installed through our main pipeline repository, here: https://github.com/dbmi-bgm/cgap-pipeline-main.

Before deploying modules from this repository it is necessary to deploy the cgap-pipeline-base module from the main pipeline repository. Please refer to the corresponding documentation in the repository.

Deploy the Pipelines

Set the credentials to authenticate to the target environment. A minimal set of credentials is required and can be defined in the .env file. Additional credentials can be required to authenticate to the environment, see here for more details.

Deploy all the modules.

    make deploy-all