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.
Quick Start Part 1: It's all about the workspace
In the FireCloud world, the workspace is the central concept around which everything else is organized. A workspace is essentially a stand-alone computational sandbox that provides a secure collaborative place in the cloud where you can organize data and run and monitor analysis pipelines.
When a workspace is created, a Google bucket is created to serve as dedicated space for file storage. All permissions on the workspace are synced with the Google bucket, so if you add a person as a Reader to the workspace, this person can read the Google bucket too. If you delete the workspace, the Google bucket gets deleted. See the pattern?
The web interface organizes workspace contents into five different views or sections:
- The SUMMARY view pulls together information about the contents of the workspace and the status of various elements, and provides options for controlling access by others.
- The DATA view displays a set of tables that contain the metadata you have uploaded (including storage location of data files) about your participants, samples, and any groupings that you might have defined.
- The ANALYSIS view enables visualizing some genomic data types using IGV, the Broad's Integrative Genomics Viewer.
- The NOTEBOOKS view enables you to launch an interactive analysis environment based on Jupyter (formerly IPython) notebooks, Spark, and Hail.
- The METHOD CONFIGURATIONS view lists the methods (a.k.a. workflow scripts) that have been imported into the workspace and provides options for configuring these methods, _i.e._defining inputs, outputs, and parameters to these methods.
- The MONITOR view lists workflow submissions, provides status information and allows you to drill down into details of their execution.