Getting started
Forking the code and cloning the repository
The OpenPipelines code is hosted on GitHub. To start working on OpenPipelines, you should create your own copy of the repository by forking it. Visit the OpenPipelines repository here and use the ‘Fork’ button on the top right hand side of the page. After you are done forking, you can clone the repository to a local directory on your computer using git clone. You can choose between using an SSH key to log in to GitHub or username and password (HTTPS) to connect to github.
git clone https://github.com/<YOUR USERNAME>/openpipeline.git
cd openpipeline
git remote add upstream https://github.com/openpipeline-bio/openpipeline.gitgit clone git@github.com:<YOUR USERNAME>/openpipeline.git
cd openpipeline
git remote add upstream https://github.com/openpipeline-bio/openpipeline.gitInstall viash and nextflow
To start contributing to OpenPipelines, you will need at Java 11 (or higher) and Docker installed on your system.
OpenPipelines is being developed in Viash and Nextflow. If you are unfamiliar with either one of these platforms, you can check out their respective documentation pages.
You can check if is installed correctly by running the following commands.
nextflow run hello -with-docker
viash --versionFetch test resources
OpenPipelines uses a number of test resources to test the pipelines. If everything is installed correctly, you should be able to fetch these resources by running the following command.
viash run src/download/sync_test_resources/config.vsh.yaml