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.
Make sure you update the release versions in the Dockerfile then build the Docker image using:
docker build -t pancancer/pancancer_upload_download .
Get this image
docker pull pancancer/pancancer_upload_download
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.
- 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.