Once you have chosen your GenPipes use option and have access to the GenPipes executable through Compute Canada server access or on your local server, you need to setup and configure your GenPipes environment as per your deployment choice. After you have configured it, you are ready to execute GenPipes.
First of all, test that it works, without actually running a pipeline, by using the –help or -h option. For details, please refer to the Getting Started Guide Run GenPipes section.
Each of the available GenPipes Pipeline has its own unique execution command. You can find details for each in the Pipeline Reference Guide. It also has sections demonstrating example runs for each pipeline.
New users may benefit from the GenPipes Tutorial section of this documentation that provides step by step instructions on how to execute a few sample GenPipes pipelines. There is also a tutorial available for running GenPipes in the cloud using Google Compute Platform.
In case you run into any runtime issues or errors, do refer to Troubleshooting GenPipes Runtime Issues or browse the GenPipes Support sections.
Happy analysis with GenPipes! We would love to hear your feedback on GenPipes or the documentation.
Contributions to GenPipes or its documentation are most welcome!