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Genomics Compliance Suite by Seven Bridges
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README.md

Genomics Compliance Suite by Seven Bridges logo

Genomics Compliance Suite (GCS) is a Shiny app built by Seven Bridges 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.

How to run the app locally

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/gcs

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

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

Run the container

If the image was pulled from Docker Hub, use

docker run --rm -p 3838:3838 --name sb sevenbridges/gcs

If the image was built locally, use

docker run --rm -p 3838:3838 --name sb gcs

Log into the app

After the container is running

  • Open http://127.0.0.1:3838 in your web browser.
  • Use the username/password sevenbridges/sevenbridges to log in.

Clean up the container and image after running

docker rm -f sb
docker rmi sevenbridges/gcs

or

docker rm -f sb
docker rmi gcs

Links

PrecisionFDA BioCompute Object App-a-thon Challenge

Copyright

© 2019 Seven Bridges Genomics, Inc. All rights reserved.

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

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