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Update the README example to pass temp_location to docker #506

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mbookman opened this issue Jul 16, 2019 · 0 comments
Open

Update the README example to pass temp_location to docker #506

mbookman opened this issue Jul 16, 2019 · 0 comments
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@mbookman
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I noticed that I was never getting Pipeline logs for my vcf_to_bq jobs. I would see in the output things like:

Output will be written to "''/runner_logs_20190716_044043.log"

Rather than a GCS path. Looking at pipelines_runner.sh, it looks like it needs the --temp_location passed to it:

  pipelines --project "${google_cloud_project}" run \
    --command "/opt/gcp_variant_transforms/bin/${command} --project ${google_cloud_project}" \
    --output "${temp_location}"/runner_logs_$(date +%Y%m%d_%H%M%S).log \
    --wait \
   <etc>

Please update the example in the README:

docker run -v ~/.config:/root/.config \
  gcr.io/cloud-lifesciences/gcp-variant-transforms \
  --project "${GOOGLE_CLOUD_PROJECT}" \
  --zones us-west1-b \
  --temp_location "${TEMP_LOCATION}" \
  "${COMMAND}"

Would also be good, I think, to make it a required field.

@allieychen allieychen self-assigned this Jul 18, 2019
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