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broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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GCP Batch runs fail with malformed docker volume arguments #7408

Open osha52101 opened 5 months ago

osha52101 commented 5 months ago

Im testing moving LSAPI runs to Batch with v86, and I keep getting the following error:

textPayload: "docker: invalid spec: /mnt/disks/cromwell_root:/mnt/disks/cromwell_root:: empty section between colons."

for this command: Executing runnable container:{image_uri:"gcr.io/google.com/cloudsdktool/cloud-sdk:434.0.0-alpine" commands:"-c" commands:"printf '%s %s\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\ container\ setup." entrypoint:"/bin/sh" volumes:"/mnt/disks/cromwell_root:/mnt/disks/cromwell_root:"} timeout:{seconds:300} labels:{key:"logging" value:"ContainerSetup"} for Task task/job-49cc8a88-722b-43067ba4-ab34-48bc00-group0-0/0/0 in TaskGroup group0 of Job job-49cc8a88-722b-43067ba4-ab34-48bc00.

The docker volumes are defined as: volumes:"/mnt/disks/cromwell_root:/mnt/disks/cromwell_root:"}

Shouldn't there be a rw permissions entry after the last colon? As far as I know, there is no way for users to modify the docker launch config to fix this. Is there something I have malformed or missing in my conf file?

dspeck1 commented 4 months ago

@osha52101 - please run this with the latest release (87). I believe this issue was resolved.