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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:
vcf_to_bq
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:
--temp_location
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.
The text was updated successfully, but these errors were encountered:
allieychen
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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:Rather than a GCS path. Looking at pipelines_runner.sh, it looks like it needs the
--temp_location
passed to it:Please update the example in the README:
Would also be good, I think, to make it a required field.
The text was updated successfully, but these errors were encountered: