make singularity volumes overridable context variables #2210
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nuwang
reviewed
Oct 2, 2024
| @@ -309,5 +309,8 @@ users: | |||
| params: | |||
| object_store_id: minio_test | |||
| [email protected]: | |||
| context: | |||
| slurm_singularity_volumes: "{{ slurm_singularity_volumes }},/mnt/aws_gateway:ro" | |||
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Why is this read-only though? Shouldn't it be writable for output files?
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write is not required for any of the other user data folders. galaxy moves the files there after the containerised tool execution has run. see volumes listed in host_vars/galaxy
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Right! I forgot the handler does the final move.
|
If this is approved, please don't merge it. I'm confident that it works but would still like to keep an eye on galaxy when it goes in. |
nuwang
approved these changes
Oct 3, 2024
cat-bro
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make_singularity_volumes_overridable_context_variables
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Rearrange slurm_singularity_volumes etc to be context variables on the default tool instead of hard coding them on destinations. This makes it possible for an aws gateway user to have '/mnt/aws_gateway:ro' appended to volume strings for their jobs.
@jlqfab @nuwang from a dry run this appears to just work.