2.3 Installing and Accessing the BCO App

The BCO App can be deployed locally and on a remote server. Both the source code and a containerized (Docker) version are available on GitHub. The source code can also be executed from the Cancer Genomics Cloud, as well as any of the Seven Bridges Platforms, through the R Studio extension on our platforms. Additional BCO App deployment details are explained below.

2.3.1 Containerized app

Running BCO App from a containerized app will allow you to execute the app without having to install BCO App requirements/dependencies on your local machine or server (Figure 1). Instructions for pulling, building, and running the Docker image can be found in the BCO App GitHub repo. The default username and password are both: sevenbridges.

2.3.2 Cancer Genomics Cloud hosted app

The BCO App can be executed from within the Cancer Genomics Cloud through RStudio, as explained in each section below.

Getting the app

Copy the ‘biocompute-composer.zip’ to your project folder. Please request access to the zip file if you do not currently have access (support.at.sbgenomics.com).

Running the app

To run the app:

  • Click “Interactive Analysis”, then open “Data Cruncher”.

  • Click “Create your first analysis”, select “RStudio” and start the analysis.

  • When the editor is launched, switch to the “Terminal” tab in the lower left panel, run the following commands to copy the app from the project to the analysis session:

    cp /sbgenomics/project-files/biocompute-composer.zip /sbgenomics/workspace/
    unzip -q /sbgenomics/workspace/biocompute-composer.zip
    rm /sbgenomics/workspace/biocompute-composer.zip
  • Go to the biocompute-composer folder in the files panel (lower right), open and run through the code in app-setup.R to setup the environment (use Ctrl + Enter to run the code line-by-line).

  • Open app.R, click the “Run App” button in the code editor panel to run the app.

  • A dialog about popup windows may appear if you’re running this for the first time, click “Try Again” to proceed.

  • Note: if running the app from a restarted analysis session, remember to run app-setup.R again before running the app.