Install your tools on the CGC

The most common bioinformatics tools for dealing with cancer genomics data come pre-installed on the CGC and are continually maintained. You can add your custom tools to the CGC to run in combination with these. Adding your own tools allows you to bring your software directly to the data, and to take advantage of the high performance computational power the CGC provides.

THe CGC supports the common workflow language 

The CGC Software Development Kit supports the native execution of Common Workflow Language (CWL) compliant tools and pipelines, so developers avoid lock-in', and their tools remain fully portable. To upload your tool, simply install it inside a Docker container, and push the image to Docker Hub or to the CGC Image Registry, which – for optimization – is hosted alongside the TCGA data. Then, using the CGC tool editor Rabix Composer, you can enter all the details of your tool's interface, including details of its command line options, and its required resources. 

Note: Please make sure to select v1.0 for the CWL version in Rabix Composer. The existing CGC web composer creates tools and workflows only in an older version of CWL (sbg:draft2) which is no longer widely portable.

Make your tools portable 

Once you wrap your tool using Rabix Composer, the CWL description of the tool is automatically generated and can be uploaded to the CGC platform, which allows the tool to be executed on the CGC as well as any other platform that supports CWL.

PERFORM INTERACTIVE ANALYSES USING DATA CRUNCHER

Bring your custom interactive analyses to the cloud with Data Crucher, which allows you to write custom Python, R, and Julia scripts using JupyterLab—an interactive environment that enables users to quickly see calculation and visualization results.