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Export folder rights


(Prathert) #1

Dear all,

I have a problem with the export folder and I am using Version 1.12.1-beta24 (build: 11508).

I am running a galaxy instance in a docker container and save generated data in an export folder on my local host system.

I transferred files from an old instance to the new export folder and changed the rights to galaxy:galaxy to allow access via my galaxy instance.
however, I realised, that a lot of novel data generated in this container get root rights instead of galaxy as it was supposed to.

see below:

drwxr-xr-x 6 galaxy galaxy 204 Aug 7 16:29 dataset_3130_files
-rw-r–r-- 1 galaxy galaxy 714 Aug 7 16:37 dataset_3131.dat
drwxr-xr-x 6 galaxy galaxy 204 Aug 7 16:38 dataset_3131_files
-rw-r–r-- 1 galaxy galaxy 21506588 Aug 7 16:46 dataset_3132.dat
-rw-r–r-- 1 galaxy galaxy 21506588 Aug 7 16:47 dataset_3133.dat
-rw-r–r-- 1 galaxy galaxy 82050777 Aug 8 07:44 dataset_3134.dat
-rw-r–r-- 1 galaxy galaxy 490588672 Aug 8 07:53 dataset_3135.dat
-rw-r–r-- 1 galaxy galaxy 0 Aug 8 08:25 dataset_3136.dat
-rw-r–r-- 1 galaxy galaxy 0 Aug 8 08:27 dataset_3137.dat
-rw-r–r-- 1 galaxy galaxy 0 Aug 8 08:34 dataset_3138.dat
-rw-r–r-- 1 galaxy galaxy 0 Aug 8 08:45 dataset_3139.dat
-rw-r–r-- 1 galaxy galaxy 384 Aug 8 08:46 dataset_3140.dat
-rw-r–r-- 1 galaxy galaxy 0 Aug 8 08:47 dataset_3141.dat
-rw-r–r-- 1 galaxy galaxy 384 Aug 8 08:48 dataset_3142.dat
-rw-r–r-- 1 galaxy galaxy 384 Aug 8 08:54 dataset_3143.dat
-rw-r–r-- 1 galaxy galaxy 2110561277 Aug 8 09:41 dataset_3144.dat
-rw-r–r-- 1 galaxy galaxy 384 Aug 8 09:17 dataset_3145.dat
-rw-r–r-- 1 root root 384 Aug 8 09:20 dataset_3146.dat
-rw-r–r-- 1 root root 384 Aug 8 09:28 dataset_3147.dat
-rw-r–r-- 1 root root 0 Aug 8 09:46 dataset_3148.dat
-rw-r–r-- 1 root root 384 Aug 8 09:49 dataset_3149.dat
-rw-r–r-- 1 root root 384 Aug 8 09:50 dataset_3150.dat
-rw-r–r-- 1 root root 384 Aug 8 09:54 dataset_3151.dat
-rw-r–r-- 1 root root 0 Aug 8 09:58 dataset_3152.dat
-rw-r–r-- 1 root root 384 Aug 8 09:58 dataset_3153.dat
-rw-r–r-- 1 root root 2110561277 Aug 8 10:51 dataset_3154.dat
-rw-r–r-- 1 root root 2110561277 Aug 8 10:51 dataset_3155.dat
-rw-r–r-- 1 root root 714 Aug 8 11:02 dataset_3156.dat
drwxr-xr-x 6 root root 204 Aug 8 11:03 dataset_3156_files
-rw-r–r-- 1 root root 387607 Aug 8 11:32 dataset_3157.dat
drwxr-xr-x 6 root root 204 Aug 8 11:32 dataset_3157_files
-rw-r–r-- 1 root root 142913 Aug 8 11:32 dataset_3158.dat
-rw-r–r-- 1 root root 404181 Aug 8 11:32 dataset_3159.dat
drwxr-xr-x 6 root root 204 Aug 8 11:32 dataset_3159_files
-rw-r–r-- 1 root root 141394 Aug 8 11:32 dataset_3160.dat
-rw-r–r-- 1 root root 0 Aug 9 07:52 dataset_3161.dat
-rw-r–r-- 1 root root 7889 Aug 9 07:54 dataset_3162.dat
-rw-r–r-- 1 root root 0 Aug 9 07:54 dataset_3163.dat
-rw-r–r-- 1 root root 0 Aug 9 12:40 dataset_3164.dat
-rw-r–r-- 1 root root 0 Aug 9 12:43 dataset_3165.dat
-rw-r–r-- 1 root root 384 Aug 9 14:09 dataset_3166.dat
-rw-r–r-- 1 root root 384 Aug 9 14:15 dataset_3167.dat

Am I missing something when I start the container? Do I have to mention that the rights in the export folder have to be different?
Thanks for your help.


(Prathert) #2

nobody observed this problem with his export folder?


(David Sheets) #3

This is the expected behavior for files that have not been explicitly chowned. See the osxfs ownership documentation for the complete ownership semantics. Perhaps the behavior should be changed so that files created in containers are automatically owned by the creating process. Is the flexible ownership of the new files causing you problems?


(Prathert) #4

I understand that this might be the expected behaviour since the files are stored on theist system. However, I was wondering if there is any chance to change this when starting the container with a -v function
Due to this all processes inside the container return an error since the instance cannot access the created file…

not sure what you mean with flexible ownership…