Download/Upload Docker Image

July 8, 2015 ยท View on GitHub

This creates a download/upload Docker image. It allows you to download/upload data from GNOS, including the VCF upload process used for PanCancer.

Developers

Make sure you update the release versions in the Dockerfile then build the Docker image using:

    docker build -t pancancer/pancancer_upload_download .

Users

  1. Get this image

     docker pull pancancer/pancancer_upload_download

  2. You can launch this Docker container either interactively or just run the vcf uploader non-interactively. The former:

     docker run -it pancancer/pancancer_upload_download /bin/bash

You can then look in /opt/vcf-uploader/vcf-uploader-2.0.5 where the vcf uploader is installed.

Also, you will probably want to mount the pem key you use into the container, see how to use the -v parameter in Docker to do this.

  1. See the vcf-uploader tool for information on how to use this to upload VCFs to GNOS. There's an example on how to call the uploader tool.