created by KateN
on 2017-04-19
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 $gatk, $cromwell, and $wdltool.
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 cromwell and 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 gatk, use --help instead of -help.
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.
Updated on 2017-07-29
From dthiele on 2017-05-15
The data bundle link no longer works and the link in the tutorial requires access :(
From Geraldine_VdAuwera on 2017-05-15
Unfortunately the access permissions to these files were restricted due to a technical error. Access will be restored shortly; apologies for the inconvenience.
From Geraldine_VdAuwera on 2017-06-28
The link to the data bundle has been updated.
From blueskypy on 2017-07-26
For sublime v3 in windows, the WDL.tmLanguage can be put under C:\Users\user1\AppData\Roaming\Sublime Text 3\Packages