CGAP Pipeline Main

This is the main repository for the CGAP bioinformatics pipelines.

Documentation

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

Initialize the Repository

Clone the main pipeline 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-main.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

Build pipeline_utils (optional). This will build from source the latest version linked for that specific release.

    make configure
    make update
    make build

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.

Test the deployment using the base module only.

    make deploy-base

Deploy all the other modules.

    makde deploy-all