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FCP-INDI / cpac

A convenience wrapper for https://github.com/FCP-INDI/C-PAC that provides a simple command line interface.
https://fcp-indi.github.io/docs/latest/user/cpac
MIT License
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πŸ› `utils data_config build command` `PermissionError` #28

Open shnizzedy opened 2 years ago

shnizzedy commented 2 years ago

Describe the bug

  1. In this figure, is the /media/12T/practice is read-write and the /media, /media/12T directories are read-only? So the permission was denied? screenshot of excerpts from `DATA_SETTINGS_FILE` and `cpac utils data_config build` output ― 이지원 Google Groups/cpax_forum: Re: RuntimeError

That's a bug! It looks like the utils data_config build command writes to outputSubjectListLocation from DATA_SETTINGS_FILE (

Usage: cpac utils data_config build [OPTIONS] DATA_SETTINGS_FILE

), but cpac isn't automatically binding that directory. In this example, /media/12T in your container doesn't point to anywhere, so you can't write to that path (/media/12T/practice in your container points to /media/12T/practice locally, but the parent directories aren't accessible from the container). As a stopgap until the issue is resolved, you could pass the outputSubjectListLocation file or directory as a custom binding or as the working directory, or run from the outputSubjectListLocation directory. ― @shnizzedy Google Groups/cpax_forum: Re: RuntimeError

To reproduce

No response

Expected behavior

cpac binds the output directory automatically

Acceptance criteria

Screenshots

No response

C-PAC version

C-PAC v1.8.3, cpac v0.4.0

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response