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runVarpipeline.sh isn't located in /varpipe_wgs/data in ghcr.io/cdcgov/varpipe_wgs_with_refs:latest #12

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erinyoung opened this issue Jul 13, 2023 · 1 comment

erinyoung commented Jul 13, 2023

Describe the bug
runVarpipeline.sh doesn't exist in the Docker image.

Impact
The README steps cannot be followed. A workaround is to download 'runVarpipeline.sh' from github and add during runtime.

To Reproduce
Steps to reproduce the behavior:

docker pull ghcr.io/cdcgov/varpipe_wgs_with_refs:latest
docker run -it -v $(pwd):/varpipe_wgs/data ghcr.io/cdcgov/varpipe_wgs_with_refs:latest
cd /varpipe_wgs/data
./runVarpipeline.sh

Expected behavior
I expected runVarpipeline.sh to be located at /varpipe_wgs/data in the docker image

In https://github.com/CDCgov/NCHHSTP-DTBE-Varpipe-WGS/blob/master/Dockerfile.with_refs, it looks like there needs to be another copy command.

The text was updated successfully, but these errors were encountered:

wchen190 commented Jul 14, 2023

Ran into the same problem.

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