pancancer/pancancer_upload_download repository overview

⁠Download/Upload Docker Image

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
   

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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
   

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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.