[AN-440] Add symlink to /cromwell_root in GCP Batch #7722
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salonishah11
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aednichols
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Apr 4, 2025
jgainerdewar
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Apr 7, 2025
CHANGELOG.md
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| @@ -9,6 +9,8 @@ | |||
| * Add 30 GB default VM boot disk size to user-requested boot disk size; this ensures the VM has room for large user command Docker images. | |||
| * Fix a bug that caused Cromwell to treat immediate preemptions as failures. | |||
| * Automatically retry tasks that fail with transient Batch errors before the VM has started running (that is, before the task has cost the user money). These retries do not count against `maxRetries`. | |||
| * Symlink to `/cromwell_root` - In LifeSciences, cromwell_root is located at `/cromwell_root`, but in the Batch backend it has moved to `/mnt/disk/cromwell_root`. To ensure WDLs that rely on the original | |||
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Nitpick - I would use "the Cromwell root directory that user scripts are run from" rather than "cromwell_root"
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Description
Jira ticket: https://broadworkbench.atlassian.net/browse/AN-440
In LifeSciences, the
cromwell_rootis located at/cromwell_root, but in the Batch backend it has moved to/mnt/disk/cromwell_root. WDLs that rely on the original path break when run on the Batch. To maintain backward and forward compatibility we create a symlink between/mnt/disk/cromwell_rootand/cromwell_root.Note: the creation of symlink does fail when run on images that don't allow root access, but in these cases the script.sh does continue to run remaining commands.
Release Notes Confirmation
CHANGELOG.mdCHANGELOG.mdin this PRCHANGELOG.mdbecause it doesn't impact community usersTerra Release Notes