Comments (4)
leepc12
commented on August 23, 2024
I will add documentation about absolute paths in README.
Caper's localization engine autouri cannot distinguish between relative path and plain string, so was not able to add it to Singularity's bindpath. Currently, it's recommended to use absolute paths only in an input JSON particularly for Singularity.
Thanks for reporting, I will look into this and fix it soon. Please use absolute paths until it's fixed.
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xk42
commented on August 23, 2024
This is affecting our environment as well. Since cromwell localization by default does hard link, soft link and file copy with cromwell. Most institutes have labs and multiple filesystems that shares data and in this case, singularity container seems to be unable to access data that are localized by cromwell and turned into relative paths.
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Related Issues (20)
- cromwell error: java out of bounds HOT 1
- Invalid or corrupt jarfile HOT 2
- exit 1
- intermediate file
- idr threshold HOT 1
- pyyaml error when create_instance.sh HOT 3
- Changing `gcp-out-dir` when using `caper submit` HOT 1
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- Failed on test data -- make_conf.py not found
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- cromwell works, caper doesn't
- Normalization
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- apptainer HOT 1
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