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Developer Documentation

To work on this pipeline, you will want to have the following installed:

  • Docker Desktop
  • Java > 1.8
  • Python 3.5.2 or higher, tests might fail with lower versions.

    • Install the following, we recommend using a virtual environment to do this, such as the Python built-in library venv:

      $ pip install caper tox

Running tests

To run Python tests:

$ tox -e py37

Running WDL tests

Make sure to set the environment variable HIC_DOCKER_IMAGE_TAG to point to the pipeline's docker image. Usually encodedcc/hic-pipeline:template will suffice, if your code changes require rebuilding then you will need to set this to point to the newly tagged image.

To run a WDL test with a specific tag:

$ tox -e test-wdl -- --tag test_align

To preserve the output logs and files from running a WDL test, pass the --kwd flag:

$ tox -e test-wdl -- --tag test_align --kwd

To run WDL tests in parallel, pass the --wt flag, here 4 indicates we want to allow a maximum of 4 workflows to execute at a time:

$ tox -e test-wdl -- --tag integration --wt 4

Linting

To lint and format code, run the following:

$ tox -e lint

Developer Guidelines

Before pushing code, ensure lint checks and Python unit tests pass locally:

$ tox -e lint
$ tox -e py36

Before making a PR, make sure that the CircleCI tests pass with no errors.