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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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AIM write-protects all of the files it makes #6

Closed coledeisseroth closed 7 months ago

coledeisseroth commented 7 months ago

Describe the bug When using the "True" flag that keeps AIM from deleting all of the intermediate files, the intermediate files created are write-protected in such a way that non-sudoers cannot delete them ("Permission denied"), nor can they move the directory somewhere else.

Expected behavior I would like to be able to delete the intermediate files from an AIM run.

Input data "rm -rf out"

Screenshots or pipeline output "Permission denied"

sasidharPasupuleti commented 7 months ago

When running as non-root user, It's suggested to use docker with -u flag. This will make sure the files that are created on mounted volumes are created with the permissions and ownership of the user that issues the command.

eg : docker run -u $(id -u):$(id -g) <remaining_part_of_the_command>