README.md

ICGC DCC - Release

Second generation of the ICGC DCC ETL build on Spark. For the first generation ETL project, please see the dcc-etl repository.

Build

To build the application execute the following from the command line:

mvn clean package

Modules

For a high-level overview of the application please see PROCESS.md.

Sub-system modules:

• Stage Job
• Mask Job
• ID Job
• Image Job
• Annotate Job
• Join Job
• Import Job
• FATHMM Job
• Functional Impact Job
• Summarize Job
• Document Job
• Index Job
• Export Job

Spark

For information how to build a custom version of Spark please see SPARK.md.

Running Application

For general instructions how to run a data processing with the dcc-release application please see RELEASE.md.

DCC Instructions

For DCC specific instructions please see internal documentation.

FATHMM

For information on FATHMM, please see FATHMM.md.