Docker with Galaxy, file permission error on network-attached storage

Hi all,

I’m getting a strange permission error when running galaxy through docker.

I’m running a docker instance of galaxy locally on my centos 7 machine and it’s having trouble accessing a folder I created on our NAS.

From docker, I can create folders on the NAS, so I don’t think the permission error is from docker.

I thought it might be an selinux issue, but I ran sudo setenforce 0 and the permission error persisted.

I feel like I’m poking around in the dark on this error. Do galaxy permissions change when running from the docker container? Is there a way to run galaxy from the command line instead of the gui?

Thanks for your help,
Josh

The traceback is here, the file is trying to create a folder:

  File "/export/galaxy-central/tools/dev_staging_modules/create_folders_check_data.py", line 393, in <module>
    main()
  File "/export/galaxy-central/tools/dev_staging_modules/create_folders_check_data.py", line 307, in main
    var_dict = make_results_folders(input_path, output_path)
  File "/export/galaxy-central/tools/dev_staging_modules/create_folders_check_data.py", line 33, in make_results_folders
    utils.create_folder_hierarchy(output_subdirs, output_path)
  File "/export/galaxy-central/tools/dev_staging_modules/utils.py", line 411, in create_folder_hierarchy
    os.makedirs(directory)
  File "/tool_deps/_conda/lib/python3.7/os.py", line 221, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/finkbeiner/imaging/smb-robodata/Josh/tmp_galaxy_testing/GXYTMP-03312021-SW-NSCLC-cas-Output/BackgroundCorrected'