General

What is GenPipes?

GenPipes is an open source python framework for large scale genomics analysis. Refer to What is GenPipes section in GenPipes documentation for details.

Where can I find GenPipes Citation reference and text?

Refer to GenPipes Citation for citing and example text for GenPipes Citation.

Where can I access latest GenPipes source code?

See Download GenPipes section of Deploying GenPipes locally in your server documentation.

Do I need to deploy GenPipes locally on a server or in the cloud to use it?

You do not need to necessarily deploy GenPipes to use it. You can use pre-installed GenPipes on Compute Canada servers. For that you need to have CCDB account. See Accessing GenPipes on Compute Canada Servers for details. If you wish to deploy GenPipes locally on your server (bare metal or virtual) or within a container, check out GenPipes Deployment and Access Guide for various deployment options and how to setup and access GenPipes.

GenPipes requires familiarity with Unix. As a Windows user, what do I need to setup to use GenPipes?

If you are a Windows user, you need to get a working Unix command line interface to start using GenPipes. Windows users have three main options to get a working Unix command line:

• Ubuntu on Windows (only available on Windows 10)

• Cygwin

• PuTTY

Also, if you plan to run genomics pipelines, you need a genomics data viewer such as Integrative Genomics Viewer, a graphical, high-performance visualization tool for genomics data. For details, refer to instructions to setup your windows laptop.

Where do I find tips on troubleshooting GenPipes runtime and usage issues?

See Troubleshooting GenPipes Usage issues section of GenPipes Getting Started Guide for details.

For new developers, are there any GenPipes development and troubleshooting tips?

See Troubleshooting GenPipes development issues section of GenPipes Developers Guide for details.