We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
(howto) Install software for WDL workshops
For our hands-on workshops, you will need to download the following programs:
The wdltool toolkit is a utility package that provides accessory functionality for writing and running WDL scripts, including syntax validation and input template generation. You can download the latest release of the pre-compiled executable here.
Cromwell is an execution engine capable of running scripts written in WDL, describing data processing and analysis workflows involving command line tools (such as pipelines implementing the GATK Best Practices for Variant Discovery). The latest release can be downloaded here in the form of a pre-compiled jar.
Our tutorial features tools from the GATK (GenomeAnalysisToolkit) to demonstrate how to write WDL scripts that perform real data processing and analysis tasks; in order to follow them you’ll need to install GATK. You can do so by following these instructions.
Please note you do not have to install everything in the linked article above, just GATK.
In order to run these tools, you will need to install Java version 8, which you can find here. To make running wdltool, cromwell, & gatk easier, you should add an environment variable for each to your terminal profile pointing at the appropriate jar files. We will use the environment variables
At this point you should be able to test that everything works properly by calling
java -jar <environment variable here> -help in your terminal for the
wdl jar files. If they work, you will see a print out of text describing what functions you can call with each tool. To test
--help instead of
WDL can be written with any text editing program, but for this workshop we will be using SublimeText. It is a simple but effective program, and you can download it here. This program also allows syntax highlighting for WDL, which you can optionally install by following the instructions here.
Lastly, and most importantly, you will need the data bundle we have prepared for this workshop. It contains the materials we will be using for our hands-on, and although it is small, we often encounter lagged downloads if everyone waits to download it at the start of the workshop. You can find the data bundle here.