Portal Pipeline Utilities

Utilities for deploying pipelines and interfacing with portal infrastructure.

For more information on available commands and how to contribute and deploy pipelines within the infrastructure check the extended documentation.

Install

The software is python based. To install the software and the required packages, we recommend using a fresh virtual environment. Please refer to pyproject.toml for the supported Python versions.

The package is available on pypi:

pip install portal-pipeline-utils

To install from source:

git clone https://github.com/dbmi-bgm/portal-pipeline-utils.git
cd portal-pipeline-utils
make configure
make update
make build

To check that the software is correctly installed, try to run pipeline_utils. If installed from source, this command may fail with a bash “command not found” error, try poetry run pipeline_utils instead.

See make info for details on make targets.