Cerise is a generic service for running workflows on compute resources, such as clusters, supercomputers, and simply remote machines. It tries to offer a consistent environment for workflows, so that a workflow sent to resource A will work unchanged on resource B as well.
To achieve this, and to offer a bit of safety and perhaps security, Cerise does not allow running arbitrary command line tools. Instead, it expects the user to submit a workflow document that refers to predefined steps built into the service. Both workflows and steps are defined using the Common Workflow Language (CWL).
Defining these steps, and adding them to the service, is called specialising the service. A specialisation of Cerise is always specific to a project and to a compute resource. The project determines which steps are available and what inputs and outputs they have. The compute resource determines how the steps are implemented. Workflows are written using steps from a particular project, and can then be sent to any specialisation to that project. Where the workflow runs will differ depending on which specialisation is used, but the result should be the same (assuming the calculation is deterministic!).
This site contains the documentation for Cerise.
Cerise can be run directly on a host, or in a Docker container. A local installation is created as follows:
- clone the repository
- git clone firstname.lastname@example.org:MD-Studio/cerise.git
- change into the top-level directory
- cd cerise
- install using
- pip3 install .
Steps and supporting files may then be placed in the api/ directory to specialise the service. For a detailed explanation, see Specialising Cerise.
To build the Docker image, use
docker build -t cerise .
and then start a container using
docker run –name=cerise -p 29593:29593 cerise
Note that the docker image gets its config.yml from conf/docker-config.yml in the source tree.
However, this will run a plain, unspecialised Cerise, which is not very useful, as it runs jobs locally inside the container, and it doesn’t contain any steps to execute. To use Cerise in Docker, you should make a new, specialised Docker image based on the standard Cerise image, and start that instead. Instructions for how to do so are also under Specialising Cerise
- Python 3.5 or up
- On the compute resource:
- Python 2.7 and CWLTool (or another CWL runner), or
- Python3 (using the built-in CWLTiny runner)
In the examples/ directory, you will find some example Python scripts that create jobs and execute them on the job running service.
Cerise follows the Google Python style guide, with Sphinxdoc docstrings for module public functions. If you want to contribute to the project please fork it, create a branch including your addition, and create a pull request.
The tests use relative imports and can be run directly after making changes to the code. To run all tests use pytest in the main directory. This will also run the integration tests, which take several minutes to complete as a bunch of Docker containers is built, started, and stopped.
Before creating a pull request please ensure the following:
- You have written unit tests to test your additions
- All unit tests pass
- The examples still work and produce the same (or better) results
- The code is compatible with Python 3.5
- An entry about the change or addition is created in CHANGELOG.md
- You’ve added yourself as contributing author
Contributing authors so far:
- Lourens Veen