README.md

BCO App

The BCO App is a Shiny app to create, validate, and browse BioCompute Objects.

Overview

This repo offers the source code for the app's Docker image, including the Dockerfile and the app built by the Seven Bridges team. The app features BioCompute Object (BCO) creation (manually or by importing from CWL workflows), BCO checksum/schema validators, PDF report generator, and an interactive BCO browser.

This README gives a brief introduction to pull the Docker image and run the app locally. For detailed usage of the app and more deployment options, please check our PDF user manual.

Installation

First of all, please make sure that Docker is installed in your system, and the docker commands are available from the terminal. If not, here is the official installation guide.

Pull or build the image

To pull the pre-built Docker image from its Docker Hub repo, use:

docker pull sevenbridges/bco-app

Alternatively, you can choose to build the image, which could take a few minutes:

git clone https://github.com/sbg/bco-app.git
cd bco-app
docker build . -t bco-app

Run the container

If the image was pulled from Docker Hub, use

docker run --rm -p 3838:3838 --name sb sevenbridges/bco-app

If the image was built locally, use

docker run --rm -p 3838:3838 --name sb bco-app

Open the app

After the container is running, open http://127.0.0.1:3838 in your web browser.

(If required, use the credential sevenbridges/sevenbridges to log in.)

Clean up the container and image

docker rm -f sb
docker rmi sevenbridges/bco-app

or

docker rm -f sb
docker rmi bco-app

Additional Resources

• biocompute: Create and Manipulate BioCompute Objects
• tidycwl: Tidy Common Workflow Language Tools and Workflows

Copyright

© 2020 Seven Bridges Genomics, Inc. All rights reserved.

This project is licensed under the GNU Affero General Public License v3.